I recently found it's pretty easy to burn all your SP in the wrong circumstances, although those were largely due to bugs or mod features.
(Specifically, I once had to special recover four ships in a single battle (when most of them should have been free recoveries), and had to invest SP mentoring/eliting new officers a few times after existing ones died)
Recovering SP is mostly a matter of finding a suitable big fight (preferably one that's easier than the XP bonus calculation thinks). Big fights are abundant (if nothing else, you can find a high-population system and pick a fight with some patrols), though not always accessible for a roleplayer (i.e. if you're non-hostile to everyone).
The idea was that you could have a very limited set of civ-grade ships boosted to a high level. The cap was deliberately low so that you couldn't, say, get the full effect on an Atlas Mk.II or a Venture, but the effect was high enough that it would have, hopefully, made some actually-civilian-ships (say, the Tarsus) more combat-capable, since they'd get the full bonus.
But that didn't really work out, and instead it was functionally *only* a buff to the already-combat-capable conversions, which in turn made those trickier to buff directly. If you'll note, the Prometheus Mk.II and the Atlas Mk.II have both received significant improvements, which I felt freer to make now that I didn't have to worry about how those might combine with the package mods.
Basically, the goal was to see some more true-civilian ships in battle, and that didn't work out at all.
In that case, yeah it was kinda flawed from the start, the true civilian ships like the tarsus even taking into account smodding in hullmods to save op just don't have good weapon layout or the op to really take advantage or consider using themselves in place of actual combat ships or even the more combatable ones like the venture and stuff. You would have to had to redesign them to have more weapon slots/OP for the packages to have been considered which prob would have been more work than it was prob worth so I can see why you didn't want to keep it around.
I think if you wanted to benefit true civilian ships more than things like Atlas2/Prom2, any bonuses the ship involved receives would have to be based on their cargo/fuel capacity. So the ship sacrifices some transport functionality for combat strength – in place of the hullmod costing OP, which it can't spare, it already has too little for vents/caps and guns as it is. Like how combat freighters are less efficient at freighting than civilian ones. Atlas Mk.II and Prometheus Mk.II wouldn't benefit as much from the conversion (but also need less of it) since they already lost most of their cargo/fuel capacity (though the Prom2 still can carry 800 fuel...)
But of course there's still no reason to do this to a Tarsus when you can just obtain and field a real combat ship, and never put the Tarsus in harm's way...
Also on the topic of Omega Weapons: is there any plans for more ballistics focused ones?
Yeah, I kinda find it odd that all the hybrid Omega weapons are basically "energy but fits in a ballistic slot". Including the ones that feel like they ought to be 'ballistic at heart', like Volatile Particle Driver (compare with Mjolnir Cannon).