I plan on taking his Pokémon for one. It should take him awhile to get them back, or at least obtain new ones so the Gym can run again. Taking an entire Gym out for quite some time would be rather interesting, don't you think?

But this is just the first step. If this goes off well, I plan on targeting Whitney next. She could very easily announce over the radio that she's allied with Team Rocket, couldn't she?