So this thread inspired me to do a pacifist, spacer start, iron man run this past week. I relied on autopilot while doing long transits in hyperspace. Just to test out the limits of the already existing mitigation measures, as well as confirm my suspicion you don't need to fight at all to do the story line.
My objective was to get to the end of the story line and enough credits in the bank to start a colony once gates were available. My fleet throughout the run consisted of the single Hermes shuttle found in the abandoned station in Corvus, fully restored after 1st exploration mission, with no guns, and militarized subsystems, safety overrides, and auxiliary fuel tanks. First skill point went to Navigation, 2nd to Bulk Transport. The run ended with the character at level 3 and with 2.5 million credits in the bank, having triumphantly returned to Galatia via Janus device.
Side note, some of the story line descriptions are kinda hilarious when your fleet is just a shuttle, and you've got a grand total of 4 crew in the fleet - including presumably, yourself. I had it my head cannon one guy talking as the engineer, then walks around me to the other side of the bridge and talks in a false accent as the navigator or communications officer.
So while in the core systems, I piloted actively, but on mission runs outwards and back in, I just put on autopilot and read a book in real life. Which meant I ran into a few fleets. In the end I payed 600 credit tithes to Pather fleets probably a dozen times or so. So at least for one of the default hostile factions, we have the option of not fighting to the death by paying what amounts to a small amount of credits relative to earning potential.
Pirates quickly became non-hostile after a few exploration missions for them, and so the reputation system can be used to help mitigate random hostile encounters. However, even before that non-hostile point, I could generally just disengage successfully, no story points needed nor any combat screen, just suffer harassment and some CR loss.
Other hostile mission generated fleets typically I also could just disengage with some loss of CR due to harassment. Or in the case of one Luddic fleet, pay off with 80,000 credits. Although transverse jump typically meant I could completely avoid mission fleets in systems. I only ended up doing one real retreat on the combat screen, which was pretty trivial given my 275 speed with maneuvering jets up (250 average speed). Fast civilian ships (i.e. frigates mostly) modified for speed instead of cargo can certainly escape most fleets just by flying up. Fleets with fast phase ships are a potential exception, although on the other hand, those are pretty rare. Given the entire enemy fleet is shown to you before you choose your action, you can know it's time to spend a story point if they are present.
I did use story line points on unique dialogues when I could, but still ended the run at 9 story points at level 3.5 (10 earned by level 3.5 + 2 story line - 3 used I think?). Didn't ever need to spend a story point to run, but it was helpful knowing it was there.
Even if at any one point all the features built into the game to keep my fleet alive failed, I'd only have been out some percentage of my credits on hand as a death penalty, and need to spend a total of about 15,000 credits to replace my ship and cargo loss. I was essentially self-insuring. Quick console test also shows if I have a fleet wipe with 2.5 million in the bank, I get returned with 2.0 million, so credit loss due to death isn't that bad.
As far as I'm concerned, the key to playing iron man, to borrow a phrase from another game, is "Don't fly what you can't afford to lose". I have learned through hard experience, if you don't want to start from square one fleet wise, don't push your fleet to the limits of what you can afford and have on hand.
In my more typical runs, in addition to hoarding weapons at a drop spot (abandoned station, size 3 colony with negative growth on a gas giant in Duzahk), I also hoard useful ships. If you're doing any sort of significant combat, the game literally throws tens of ships at you as salvage, so every time I return to my stash, I drop off another ship or two I've picked up. What I have in storage generally outpaces what I have in my fleet - I'll typically have unused d-mod capitals before I've actually decided to transition to using capitals in my fleet. It means my active fleet grows slightly slower perhaps, but my progress only gets set back a few minutes instead of out a few hours in a fleet wipe or fleet retreat situation.
Anything less than losing a fight outright just means I've got some new d-mods or I'm out some credits doing restores. Ships can be made guaranteed recoverable in many ways, so it is entirely within the player's control to ensure "can't afford to lose" ships are not permanently lost due to a single mistake in combat.
Finally we come to arguably the easiest but most time intensive to acquire resource, story points. I feel these require some discipline in their use, or at least experience and feel for their rate of gain. I typically keep a healthy margin on hand, like 5 or so, as well as not flying all my s-mod ships at one time. By level 15, you'll have earned 56 story points, and I typically don't need more than 20 s-mods in an end game fleet (perhaps 30 if I'm running special modifications), depending on skill choices. That still leaves another 20-35 story points, just from hitting max level, that don't necessarily need to be invested in your primary fleet. So at many points I'll be sitting on a pile of already s-modded ships in storage, as insurance against the worst case. Or have the ability to s-mod up 4 capitals quickly.
I feel like experience in iron man games make my non-iron man games better and faster simply because I don't reach for the reload button, and I just roll with the punches. I also evaluate threats much better. In that sense, consequence in iron man has become one of my better teachers for the game, and forced me to incorporate a lot of the less used mechanics the game has. I save time by not replaying the last fight 3 times to have no losses, when instead, I could have had 2 more fights in that time and made enough credits to restore the ships from the 1st fight. It wouldn't surprise me if some people replay several hours worth of game time via save/reload over the course of an entire campaign, given late game fights might be 10 minutes or more real time each. Or depending on how often they makes saves in long play sessions.
So in summary, I feel like a lot of the suggestions can already be done in game with the tools we have on hand. Story points are essentially universal currency to "buy off" any hostile fleet. For factions for which it makes sense, you can also sometimes buy off fleets with credits. A fleet of sufficiently fast civilian ships can simply disengage without ever going to the retreat screen and just pay some supplies. Insurance can simply be done by holding a reserve of credits along with ships and weapons in storage. With experience, the already existing campaign layer can be used to mitigate a wide variety of potential losses at the combat layer. Could the game use some more tools? Maybe? I'm only a single player with experience at my skill level, so I can't speak for everyone. Over time, I've come to realize the most recent versions of the game do at least give me the tools necessary to mitigate a total loss, or avoid it entirely.