I was under the impression that magic and Overgod skills fulfill different roles. Magic is mainly for offensive purposes, though it has some support abilities, and Overgod power is more for healing and support abilities, though it has a few offensive abilities.
From a story perspective, the party is trying to stop the Cult from breaking the Overgod's seal on the Creators. Even though they're using magic, they're still doing something beneficial to him, so he would probably still continue to lend them his powers. William, in particular, has been a faithful member of the Church all of his life. The Overgod isn't just suddenly going to stop allowing him to use his powers because he has started using magic.
I think that equipping Titanium should significantly increase Magic Points, but decrease Overgod points (Focus Points, as you called them.) We would still use both types of MP. This would add some strategy to equipping characters with Titanium, as the player would want to balance between the two types of skills. Maybe they'd try and keep all of their characters balanced somewhere in the middle, or maybe they'd give some characters a lot of Titanium and magic, while giving others none so that they retain their powerful Overgod abilities. It would add a unique strategic aspect to the game, so I think we should keep it.
This is just my opinion. It's probably not presented very well, as it's almost one in the morning here so I'm not entirely awake, but I think you get the jist of my perspective on it.