Personally I'd only mind the UPS/memory hit if it brought me well below 60ups, I assume that would only happen close to megabase scale though, where you're already expecting sub-par ups.
Yeah I'd prefer that they heal even after combat if they're damaged. I'm still pretty early on in my first game with Rampant though, getting through blue/military science right now. Don't know how bad the biters will get later on.