I'm having issues with the defend mission not showing up on the map properly. I use the C2ISTAR module to auto-task blufor againsta fia opfor. Is there anyway I can exclude certain missions from being generated?

This should be possible - take a look at the Sabotage demo mission that is supplied with the mod - there is a line in the inti file there that permits only Sabotage missions - see line 145 of init.sqf