Lucky for me, I always research mk2's and mk3's so i just rebuild them when they get stupid and think they can fight.
I do research them late game. I just happen to have an army with 500+ parasites in it, so most of my militia is made up of stolen units (having a full compliment of Mk3 bombers, fighters, and frigates without having the ability to research them (I don't have the knowledge) is awesome; then add in a compliment of Mk3 electric shuttles).
Also, the Mk2 that died was originally mine, it turns out. I'd only stolen 3 Mk
3 engineers, all of which are still alive. In any case, I recently stole another 10 Mk2s (the Mk3s escaped).