Satchels and teamkills.
I've found that playing an engineer and dutifully blowing up doors and windows for easier access to objectives can be a bit of a gamble. Even calling out your intention and warning people to stay clear is often not enough to avoid one or more teammates being caught in the blast. I've even seen people run up to my satchel and stand there looking at it even as I'm diving for cover.
I'd suggest an audible warning be given when a satchel charge is primed. Characters will yell when a grenade lands near them, and a satchel charge is no less dangerous. If, and possibly even if not, implementing an audible warning would require too many resources, I'd suggest being killed by a friendly satchel charge no longer be counted as a teamkill, as long as an objective such as a door/window was also destroyed in the explosion.
The opportunities for griefing if the above idea is implemented should be fairly minimal on the current maps, especially if an audible warning is also given. After all, you can only blow up each objective once.