I'll step up to the plate!
on one side of things, Serenity explicitly states that their falling in love is forbidden by law of God, so there is that, the results of their love could have been a form of divine punishment, although a rather harsh one all things considered. So while I'm not usually one to deny true love, when the fate of not one, but two entire civilizations is at stake, smiting the laws of a divine entity isn't usually a good idea.
That being said, you're right that their love did end up defeating Metalia. But who's to say that there was no other way?
So while I am for their miracle romance, while I do believe that they both genuinely love each other, I don't really think they were in the right to put the lives of all of their citizens at stake.