Gooral, I respect your opinion - and for that matter, anyone who has different or equal opinions -, I would just like to ask you if you thought about the situation this way:
Roy did have a choice at the Ishval war - kill or not kill. But, what he really wanted to do was change the military and the way the government was, and that would require him being at the top of everything. To get there, he first needed to gather information on how things worked, so he could find a way to change everything, since no one else (at least apparently) was doing anything to change the country and it's ways. He did what he was ordered so he could stay in the military - maybe even be promoted - and get the knowledge he needed to do what he is trying to do at the moment: change the country, save future lives both of Amestris and other countries that the current government would try to overpower. To do what no one else seemed willing to do, he decided it would be better to kill a few thousands in order to be able to save much more - this is what I believe the character thought and is what Arakawa tried to convey.
The point here would be almost like the point made by Alan Moore with Ozymandias in the Watchmen novel - sacrificing a few to save many, since if nobody did anything, everyone would die - if I am seriously wrong about the novel, someone please correct me.
That was Roy's objective, and what gave him the steady head to do what he did at Ishval - I believe.
Here, with Envy, at that moment, he didn't have any rational reason to kill him, except satisfy his desire of revenge. I believe he wasn't thinking "Envy, if I don't kill him, will go out there and kill many more", or trying to save anyone. He looked as if all he wanted was to make himself feel better - and this is not something a selfless, rational, coherent and trustworthy ruler/president should do. Caligula is an example - he killed people just for the heck of it, because he wanted to. The problem here is that Roy was doing something that neither he nor Riza, Ed, Hughes - and everyone else who backed him up untill now - agreed with, but he was overpowered by his emotions (again, a flaw when making decisions involving many people) and if it wasn't for Riza and Ed (Scar to a lesser degree, I think), he would have fully turned into a hypocrite that would be unworthy of ruling the country in the eyes of those who backed him up untill now - including himself. This would result in loss of trust in him, and all that they are currently fighting for - to change the country - would be useless, since the person they wanted leading the country is unworthy of such a position, as he would be unstable.
So, I believe this is the reason that the scene is coherent, and in my opinion, very well made. If you have thought about this point before, I am sorry for using a few minutes of your time. Again, I have no problem if you disagree
