I have destroyed the Institute using the minute men, but I also gave the data to the BOS, I still have access to the minutemen, railroad and BOS repeatable quests, and according to what I have read the BOS should have attacked the castle. Note that I can no longer talk to elder Maxon or preston for missions, preston still talking to me about the max affinity conversation.

Also note that I started but didn't complete liberty prime quest and did the railroad underground undercover quest up to continue working with father