Okay, maybe that was an exaggeration, but the only exception I can think of is the recent Doom remake. That does go out of its way to encourage you to play aggressively. The key word here being "encourage". One of the general overarching issues Starsector has that I've been harping on here is that it doesn't encourage anything, it shapes the player's experience predominantly by punishments and penalties.
Doom Eternal punishes you a lot in service of the same goal as Starsector: Using the game's entire arsenal is fun. Mancubi's smash attack destroys you up close, so you can't just run around with the super shotgun. Better falter him with a grenade or snipe weakpoints or microwave beam freeze. Killing four buffaloes with 3 paragons leaves you vulnerable in a future fight, better design a nice hunter-killer group of frigates instead of just a battleship doomstack and some escorts. In fact I'd say Eternal punishes you much harder but its apples to oranges.
The other major issue with removing CR is that its a base mechanic of the game. First, CR functions as the main "you took damage on the campaign map" meter. Of course you could just replace all instances of CR damage with hull damage but that both shifts the game's balance and complicates things. What happens if the hull reaches 0 on the campaign map? CR damage has roughly equal effects across ship type, but the impact of less health differs drastically between ship types.
Speaking of balance, CR is a huge part of that too. What do you add to balance out high tech ships/SO, etc.? Your proposed safety mode seems rather unjustifiable lore wise. Removing CR would essentially require a total rebalance of every ship in the game, which seems rather overboard.
while I don't like deploying everything and then traveling for ages to replace the supplies that wasted.
I don't really understand this argument. Past the early game supplies are cheap, you salvage more from fights, and you have oodles of cargo space to carry extra.