Wow, totally different situations in every case. The Horta was defending her race. The Gorn thought they were doing the same. Vaal's people were acting under compulsion, while Vaal in fact was destroyed. Rojan brutally and unnecessarily killed defenseless Yeoman Thompson solely to punish Kirk for his escape attempt. That makes him a war criminal. And contrary to what you seem to be espousing, many peace treaties provide for the punishment of war criminals from the losing side.
No, offering to take the Romulan commander prisoner wasn't wrong. In fact, it's exactly what I'm suggesting should have happened to Rojan. And finally, no one said Rojan should be killed.