I'm heading to the linkup now. Though I somehow doubt there are multiple endings to this game, here's what I would take into account when making my decision:
-Chances are, in both scenarios you still have to go to hell (either end the infestation or find what Swan wants.
-Chances are, in both scenarios, it's still a single man mission.
-IF I was going to get help when going into hell, I'd rather be at the point of an expeditionary force of Marines than some loose cannon with a BFG.
In either case, I have trouble believing you have a choice. I'd go back and replay it to see if you can actually do both.