Yes, there were hard choices to be made and, in my opinion, Reyes made the wrong one. Instead of saying "They will not come for you." instead he said "We will let them come for those people over there instead of you". Was it simply because they were forming an independent colony and not a Federation protectorate? Would he have decided differently if they had stayed in the Federation?
Starfleet may have put themselves in harm's way but it was not in the protection of life but rather in the protection of secrets. Of power. Of something that would give them an edge over people who were different from them. Sadly, that included hundreds of innocent civilians.
In hindsight I think Reyes would have chosen to break his silence if he had the chance to do things over. Sadly, all those people had to give their lives in order for him to learn that he was on the wrong side of things. However, just because he learned a tough lesson does not excuse his initial mistake in letting civilians go into harms way without all the knowledge of the dangers they faced.
Nogura on the other hand simply tried to deal with the cards he was dealt and didn't let the consequences change his mind. He seems to be the sort that feels you cannot make an omelette without breaking a few eggs. The crew of the Omari Ekon and the scientists of the Vault just happened to be the eggs in the carton he had. He saw the consequences and he moved on, unmoved. As opposed to Reyes I feel that Nogura would do everything exactly the same way that he did. Right or wrong, he stands by his decisions.
In a modern setting, Nogura was G.W. Bush or Dick Cheney and Reyes was Colin Powell, although Powell waited until he was out of power to admit he was wrong.