I think lots of small groups in T2k would be called SOF, but aren't 'true' SF (ie. Q course, etc.). Just small groups of infantry/scouts that work well together, that would be given missions that would traditionally go to 'true' SF units. Actual operators would be exceedingly rare I'd think, for the reasons you outlined - they'd all be dead/stranded/etc.
When I used to GM (I would now, but can't find players!), I let people be SF if they wanted. Generally though, I had good players that didn't abuse it. I'd make them come up with a real good story of how they got to where they were, etc. I never played an SF player - it's kind of like playing the game on 'easy mode'
