Well. Each faction in fallout 4 has that morality question involved like a running theme.
I.e;
- the brotherhood will outpace the scarce resources with the need for their tech and destruction, after the institute they will find someone else to destroy and assimilate the tech
- The institute will push science beyond morality constraints
- the minutemen are a mess structurally at the moment and could even be seen as an infintary BOS, which.. May not be a good thing.
so.. My only thought for the railroad was "if i free all the synths, their ultimate goal.. What then? Do they find a new enemy to terrorise and change the entire organisation or disband?"
Because far as im aware, thats the only goal. And if their ending has you liberate the place synths are made then they've completed what their intention was and, as a result, would have no other purpose.
What would they do? The thought of a built up group in fallout just going "**** it! I am done."