Is it possible to script an either/or senario into the campaign? More specifically, I was thinking about either killing a civillian transport or letting it escape. It would be a kill objective with a timer. The attacking team wins if they kill the transport or if they wait the timer out. The problem is that I want the game to show a different message depending on whether you killed the transport or let it go and i'm not sure if thats even possible.

You can use variables. Have two (event1, event2) and if one event happens (say the transport is destroyed) set it to one. Then use if event1 == 1 then or setting the other to one to control what message pops up.