The thing is, they're not former enemies. They're still current enemies that they would not accept clemency and would continue fighting had he not enslaved their lord- because they're subordinate to a higher enemy, and THAT main enemy has as strong if not stronger claim to the throne than he does (since he only became king from the whim of the former one, if we look at it from an outsider's perspective), and as a "realist" you have to deal with enemies decisively, so it's entirely reasonable to deal with them harshly while at war.
He DID say that he would resolve the problem AFTER the war, in this I think he's reminded of people like Julius Caesar who during the civil war would prefer enemies alive so they could be pardoned after he's won the entire war, letting the people know just what a GREAT and NOBLE and MAGNANIMOUS guy he was. That's arguably the real reason he cried when he saw Pompey's head, because he's dead and now the civil war won't be ended in a heartwarming "Well, it sucked that we had to fight, but now that I won I guess you can see that my way was right all along, so let's bygones be bygones" moment.
GRANTED, Julius got his head cut off by those same spared people. So I'm guessing MC is going to go try and be magnanimous after he wins, but will be more pragmatic about it in the end.