Ewww. God no. No minigames please
Minigames are immensely immersion-breaking for me, and the whole personel management thing drives me batty.
These sorts of "balancing measures" never really work out like that. Minigames, you're either very good at(or become very good at) in which case they add no difficulty only annoyance, or you always struggle with them in which case they just make things needlessly difficult (and also annoying).
Every game with these "minigames" to accomplish actions always ends up that way.
Also, this forces ship capturing/salvage/recovering into being a direct player action and not possible OOS; or creates a wierd situation wherein you've got to jump though additional hoops if you are IS.
A option (which can be disabled!) that I'd like to see is a way to have derelict ships decay. Say, have all ships without pilots that are also below, say, 25% hull continue to loose hull points (a percentage of the total amount) after bailing. This would negate the need for (though you could still use) NPC salvagers, ensuring that the universe doesn't fill up with derelicts. This could be written off as a self destruct mechanism, as you note, or simply the effects of catastrophic battle damage and no on-board crew to repair/keep the ship together.
I'm not concerned with "too easy". The "easy" factor is really going to be set in the likelyhood of big ships bailing in the first place. The trick is to get lower percentages to actually work well, so huge ships are very unlikely to bail *but* will occasionally bail with sufficient hull points remaining to survive incoming fire.