How would a pro MMA fighter fare?

probably win

depends on the situation.
you know when a lot of these american "masters" bang on about how they would break their opponents limbs or take out their eyes etc in a street fight?
well a spec ops commando who's had a lot of experience in the field probably would have found himself actually applying such techniques to resisting opponents. You're average martial artist would never have such an opportunity and has probably never found himself fighting for his life. That goes for pro fighters too.
As aggressive as a pro fighter maybe, chances are he has never had to kill anybody.
Not saying an MMA fighter can't fight dirty, but they would have less experience fighting in such a manner.
Anyone can say "I'd gauge his eyes out in a real fight" but in reality its not that simple. I doubt a pro fighter has what it takes mentally to do something like that.
In the ocatgon I would pick the MMA guy any day as special ops are trained to kill, not to submit opponents. But out in the field, if the special ops need to eliminate a pro fighter, it would only take 1 of them with minimal effort. Chances are they wouldn't mess about with hand to hand combat.