No, unfortunately it can't.
Is there something different with FSME missions than *.SCR files?
I don't have EAW anymore but isn't it as simple as creating an .MCT file with the listed *.scr missions created from FSME?
Personally, I'd experiment by copying one MCT file and renaming it and then saving it after writing in the new*.scr file names.
For example, this process described below should work the same for any SFC: EAW mission.
In SFC:OP I have one of Tracey G.'s Doomsday Machine missions.
I copied a Klingon Campaign MCT file and renamed it "Doomsday Machine Campaign" In the MCT description section I add something like "Hunt for and Fly against the Doomsday Machine." I then save it as a "Doomsday Machine Campaign.MCT" file. This text later appears on the campaign selection screen.
In the actual MCT file, I replace the name of the current missions with:
"Doomsday machine.scr"
Note, I do not alter any of the mission order numbers or anything other than what's in the quotes. I tend to remove extra missions as I don't want to play 50 OTHER campaign missions before I get to battle the planet killer.
I then save the renamed MCT file and can then start the game and play the Doomsday machine Campaign.
Please also note that EAW and OP missions are NOT interchangeable.
Qapla'
KF