I'm referring to:

Randolph Safehouse

Operation Ticonderoga

Variable Removal: General Atomics Factory

I'm siding with the Institute.

Whenever I go to the locations of the above quests I have instructions to either kill Synths or kill a Courser.

Obviously when I meet them these Synths and Courser are friendly to me.

I want to do these quests, but not if doing them makes me an enemy of the Institute. I don't want to get locked out of the Institute.