One of the first playtests I ran was a series of three games featuring SG-1 against a Goauld minor lord, his Jaffa bodyguards and a few local 'viking' worshippers.
As our beloved SG-1 began to fall we came up with an elegant solution, SG-1 are effectively immortal. They can be downed but then that allows them to be captured and then form part of a later escape mission. Downed SG-1 members that are not captured are just wounded, or knocked out.
Daniel was captured like this in the first game. The next game was then a mission to rescue him by SG-1, 2 and 3. Made more complex by the inteference of the Lucian Alliance. It was great fun.
With a skirmish game make your objectives simple. Put down a counter and say it is a data crystal. Or make SG-1 have to wait two turns by an ancient artefact so Daniel can decipher it.
"Youth and Talent are no match for Age and Treachery".