Let me break this down:
-they don't have very good or consistent evidence that the Synths they are "freeing" are self-aware (almost all the Synths I talked to before they had their memories changed showed very little indication that they were).
-they effectively kill the Synths by giving them entirely new memories and personalities. While their reasoning is understandable, not having the time to teach every Synth how to act human, it is negating the point of "freeing" the Synths since they are no longer the individual who "wanted to be free"
-they have you destroy the Institute. Not only does this mean killing entire families but also resigns the Synths to eventual extinction as no more can be produced. This completely negates the reason for the Railroad's existence
-they have you kill off the Brotherhood of Steel to protect, maybe, a hundred Synths
-on top of all this they don't do anything to aid the rest of the Commonwealth
So in the end siding with the Railroad:
-has you commit genocide against three groups, including the ones they were formed to "help"
-leave the Commonwealth without a faction to keep the Raiders, super mutants or Gunners in check (the Institute did even if it was for self serving reasons)
Not really a good option is it?
Or am I missing something here?