Although he isn't on your team's side the whole game, I never considered Jowy a bad guy. He did what he felt was neccessary to end the war, he just felt that doing it from Highland's side would be easier than from Muse, Two River, Greenhill and Window's side. He figured since Highland and Harmonia had such strong ties, hed get them to help (he did with Sasarai and even got the Grassland's help too. Lucia, Hugo from 3's Mom, was the assassin hired to stop you from facing highland). He didn't bank on the unification of Tinto, Two River, Window, Greenhill AND recieve help from Gregminster in the Toran Republic. Add the fact that all of Camus and Miklitov's Knights joined too (leaving the Matilda Knightdom). Highland was far outnumbered.
At the point in which Jowy leaves Namami and her brother, it was apparent Highland was in control and it wasn't going to get any better for Muse and the other regions. Jowy did what he felt to stop the war. He wasn't an enemy like Luca or Neclord were.