Ending the Railroad is the only way you can become Director though, otherwise no-one in the Institute will trust you as your motives will be viewed as highly suspect. Plus it's only like 10 people, who would kill you in a heartbeat if they got the chance). its not like you're nuking a vault full of men, women and children *cough Brotherhood*

All the quests have a, "What the hell, Faction?" quest

1. The Railroad quest has you discover they intend to blow up the Institute with the Mass Fusion device in addition to their revolt to free all of the Institute's slaves.

2. Danse's betrayal by the Brotherhood

3. The Institute sending you after a bunch of runaway slaves to return.

I prefer having some factions be good and idealistic, some being evil and ruthless, some being morally grey but logical and understandable. I didn't like how every faction in Fallout 4 is just a group of closed minded and murderous fools that all want to kill each other. I also didn't find the faction storylines to be interesting enough (Skyrim and New Vegas did faction storylines much more suitable to my tastes). I didn't feel compelled to side with any of them, I didn't feel like I even had a reason to be involved.

I updated my "Moral Ambiguity of Fallout 4" essay if anyone wants to read it.

http://unitedfederationofcharles.blogspot.com/2015/11/the-moral-ambiguity-of-fallout-4.html

I added more information about the Institute's difficulty at reforming, the Minutemen's supply issues (as well as the Commonwealth's status as ungrateful bastards), plus things like the BOS' purpose being thwarted.