Currently, if you manage to enter sneak during combat, armor is replenished only if the AI decides to cast a spell like Fortify. Armor will only regenerate upon leaving combat, but health will not.
I don't understand why the devs didn't make it so that health regenerates as well. Stabbey's fix is simple and obvious, but like you said: "If you kill someone they will stay dead".
I don't care if it's "boring" or "cheese". I should not be able to use sneak and marksman's fang (or another piercing attack) to deal free damage out of combat, and only enter combat for the final blow to earn the XP. This is a simple flaw that can be addressed with Stabbey's suggestion of regenerating health if the entire party is out of combat. It shouldn't be difficult to program, either.
It's true that freezing cooldowns while sneak/invis is punishing...but I wonder how punishing it is exactly, especially in a party of 4, where if you're playing a squishy melee you are constantly getting buffed and healed.
Also, I just realized, any kind of targetting should break invis. Maybe that is the real fix. It only makes sense that your position is revealed if you are targetted by a spell.
Something else I've been thinking is that maybe combat sneak should only be available to characters with points into Scoundrel. It might work like this:
if Current level + Scoundrel level >= Enemy level, then sneak is possible during combat.