Is it justified morally? No.
Is it justified by the Brotherhood's logic? Yes.
The BoS thinks synths should be destroyed, even non-Institute ones. The Railroad helps synths. Therefore letting them live makes their job harder.
@Repoman100
Any actual sources for your claims? Since, you know, synths are sentient. Not like smartwatches. And that the Railroad never states they will kill all humans to save synths. Meanwhile, the Institute says they'll kill everyone else to achieve their goal...