So i'm doing this quest with Deacon to enter their old base beneath the Donut Shop and so it happens that i've already been in the Institute and all the synths in there are friendly to me, but Deacon doesnt know like anything and tries to fight them. Right know i'm standing behind 4 sythns that are trying to fight with Deacon. So what do i do? Because i like to complete most of the quests before completing the main one even if I do't like Railroad because they bunch of [censored] idiots. Can I just kill those synths and later they'll okay with it and still not attack me? Or should I just say [censored] Deacon and just him in the face because there will be more quest with synths in play?

As far as I can tell, killing random people doesn't really affect factions overall. I remember once I was wandering around outside Diamond city, it was dark and raining and I spotted some guy asleep in one of the buidings. I pulled out my sniped and blew his head off. When I got over there turned out it was Diamond City security guard. But nobody mentioned it, another guard even walked by as I was looting the corpse and he was fine with me.

just kill the synths. It wont effect your standing with the Institute. Honestly i like Nick Valentine a lot more then Deacon.