Deacon mentions there is contention within the Railroad about what constitutes a "synth worth saving" for lack of a better term. Gen 2s are the ones you are blasting away most of the time I believe (someone correct me if I'm wrong) and Gen 1s are really rough, I don't believe they even have a coating for their chassis. They are just the mechanical nuts and bolts.
To me the issue isn't what generation they are or what they look like, it all comes down to the idea of possessing a soul. In all my interactions with Valentine, it is very clear that he is a person, not a thing. So regardless of where he falls on the generational timeline, I would consider him a synth worth saving. If Gen 1s and 2s lack that personhood, then it makes sense to me that there is contention about whether or not those synths are actually worth the time to try and save.
Also, I think it needs to be firmly grasped that the creation of an artificial life and/or intelligence is something that has no true real world corollary. Popular movies and fiction (of which we can include Fallout) have delved into the realities and evils that would arise from these types of advances and so they serve as sort of fertile ground for discussion. I find it highly improbable that we will ever create a true A.I., but cloning could certainly be possible. And how will we treat clones? If you've never seen Moon with Sam Rockwell, I think you should give it a watch. Very heart wrenching and thought provoking. That to me at least parallels slightly the situation we have here. I have several theories for why the Institute was even trying to make synths, none of them pleasant, but the intent of their creation is subordinate to the reality that they are essentially people. Even if you uploaded their consciousnesses to a calculator, that would not make them less human, it would just mean their physical form is not human. It is a concept most people aren't comfortable with, but I think the two biggest reasons people don't like synths is because 1) they are BoS bros and its part of their M.O. to hate/kill them so what can you do and/or 2) the idea of synths are so unsettling and it is simply a fear of the unknown response. It might be a threat so we have to destroy it now! Both strike me as weak reasonings, the first being especially egregious.
Synths don't have children (not sure if they are incapable of it since they are mostly biological human material) and as for killing members of a group, the RR does if we are counting Gen 1s and 2s, but that is always in self-defense, so we would be talking about preventing births in this case. Again, as I said before, I'm not sure that the substance of this provision or law necessarily correlates well with the scenario we have presented by the Institute and the creation of synths. It is very true that the Institute is the only organization capable of creating new synths, but you would have to ask the question: do synths want to form their own society? And most pertinent: can they reproduce with other human beings? How human they actually are is never directly addressed but you can obviously have six with a synth, so if they are human enough to conceive, then I think this is a completely moot point. I mean that is the whole goal isn't it? Get them out of the Institute, give them a new identity, and then send them outside of the Commonwealth. In the end, they shouldn't realize that they aren't human and they should be able to do whatever they want. Knowing that is the end goal of the Railroad makes me more comfortable in supporting them. If they were trying to make some kind of New World Order with the synths (which is something I suspect the Institute is(was) trying to do) then I'd be hesitant.
I think the key to this question is an unspoken statement that the leaders of the Railroad never make. They know synths aren't natural. They know that the people of the Commonwealth don't want them in their home. However, they recognize that synths are persons and therefore should have all the rights entitled to persons. You can't tell me that they don't recognize that destroying the Institute is going to make it so there are no more synths to save, and that's because saving synths is not their business. This is a humanitarian underground movement, not an organization with a yearly quota. And that's what confuses me when people say the Railroad has short sighted goals... duh lol. Their goal is short sighted because it is readily obtainable. Destroy the Institute and free synths. End. They might re-purpose themselves afterwards, but they could just as easily say: "job done, go home everyone".
So, in essence, I don't consider it a genocide because if they can mate with human beings and conceive, it isn't really preventing birth. Obviously, true synths cannot be made anymore, but I'm not so sure that is something even synths would want. Most importantly, this is completely new ground and as I said before, I'm not sure how we apply an international law like the one you mentioned to this fictional, hypothetical scenario. It doesn't seem as though it lines up quite as nicely.