AFAIK there is no way to revert to an old mission and continue the campaign from there. Once you accept an outcome of the mission, it's final and irreversible. You could of course modify the save files manually with 3rd party text editors, but that's a different thing entirely.
There is some speculation that shooting the transport originally resulted in a failed mission, but in the end both outcomes became accepted as a success, even though the debriefing is very harsh for the "shooters". However the rest of the FS2 campaign doesn't really change according to your choice, so you can safely continue playing to the end.