Biology, Chemistry and Physics would have to say they were wrong as a start.
If hydrogen and oxygen combine to form water simply because some God or Designer decided that's how it would be until She changed her mind it eliminates all we know about chemistry.
If lightning is really just the result of God getting pissed then we need to rethink all we know about physics.
Well, if they were
simply those things or
just that, then I suppose you're right. But the existence of a creator doesn't necessitate those things.
Chemistry describes the interaction between hydrogen and oxygen whether some deistic-type god set the universe in motion or not. Its only when they'd be directly controlling those interactions themselves, and they change something about it, that it would become a problem for chemistry.
™ Version 4.2