I've only played once and I sided with the BoS. It's kind of a BoS-MM alliance except Preston is extremely disappointed in me for blowing up the Institute so thoroughly and reminds me of this every time I stop in to say hi.

I don't think it's bad for the Commonwealth? Maybe the opposite MM-BoS might be better. I mostly sided with the BoS for the cats. And Danse and Ingram :)

I need to play Railroad and Institute so I can have a chance at befriending their companions!