Officially, the Magico government is not affiliated with the Magical Girl Union, but Presidente Santos has been giving it a lot of support in the background. Which means that if the new president isn't interested in doing the same (and he isn't), that's going to make things harder.
If a president of Magico wanted to actually attack the Union, that would definitely be worse, because a president could pass some laws banning it outright. But fortunately, the new president is just pretty apathetic about the whole thing -- he won't stand in their way, he just won't help them.
By the way, fun fact: the warmonger has shown up once before. On this page! You might see now why Chronos said he could be a disaster.