Disclaimer: I don't play Fallen Spire.
I am generally extremely conservative with my forces, and reload if I do something stupid that causes a fleet loss. So, I don't mind reprisal, because I generally don't get a ton of reprisal waves.
On the other hand, AI War Classic generally makes me feel extremely time pressured. Even without AIP auto-progress, the knowledge that exos are charging and ever-larger CPAs are coming makes me want to win as fast as possible. That's part of why I am so conservative; refleeting takes time and time is AIP. This is especially bad in the early game when metal is still very tight.
Reprisal significantly alleviates the time pressure around refleeting, so to the extent that it feels like a reliable way to recoup moderate losses, it might actually make me play MORE aggressively. That would be good!
Reprisals do seem hard to balance due to their tight integration with salvage, given that salvage also interacts with other mechanics like waves. IE, you want to balance reprisal waves to a nice level of lethality, where they never feel fully safe but only a full fleet loss risks killing you, or whatever. But, that might make them give too little salvage to assist with refleets. You could buff salvage rates, but then people run their whole economy off the salvage from regular waves, and other econ unlocks become less attractive. Waiting for large reprisal waves means you don't get any help refleeting from moderate losses.
So, you might want to decouple the 'make refleets faster' and 'make refleets less boring' parts of reprisal+salvage. Or, add knobs so that you can tune reprisal => salvage metal conversion differently from regular waves => salvage, but that's gonna get messy.
If people are having to throw fleets into grinders to make progress, then that may indicate more of a problem on the tactical side of the game. That's why Sabotage Hacks were added, to avoid horrible gordian knot defenses on the AI side. Fallen Spire seems especially prone to fleet => wipe => refleet, from what I've heard, as well as not feeling very tactical. Maybe those problems are related?
Morale seems like a worse kick in the pants than reprisals. Reprisals mean you get your teeth kicked in *somewhere else* where you aren't getting wrecked. If you're doing badly on a planet, because that planet is a brutal nut to crack, then you don't need a mechanic that makes it HARDER to crack the longer you fail. I mean, unless the intent is to encourage players to give up and use Warheads.