I really don't think he had anything to do with that.
While I don`t know if Clover`s closure is his doing, I`m pretty sure Inafune did everything he could to antagonize Clover. And not just them. Reportedly, Inafune was the main reason for Yoshiki Okamoto leaving the company. Also, he was the one who pushed for the PS2 version of Resident Evil 4 practically forcing Mikami to resign.
While he wasn't involved (as far as I know), Zack & Wiki is a wonderful standout game from Capcom, so I can't really hate them just because of the incident with Clover.
Clover`s closure is just the tip of the iceberg though. A lot of talented staff have left Capcom over the years and Capcom did nothing to prevent it. There`s a relatively recent interview with Yoshiki Okamoto on Gamasutra in which he implies that a lot of people continue to leave them even now. And if the news of Street Fighter IV being developed by Dimps is anything to go by, I think it`s safe to say Okamoto is telling the truth. Capcom`s excellent 2D artists have also probably long left for the greener pastures of SNK and Arc System. What with Street Fighter II HD remake being done by Capcom`s US branch and looking ugly as sin(I think the first Fatal Fury had more frames of animation than this).
Lame they didn't include the original credits in the Wii version though.
Yeah, it`s by far the best staff roll I`ve ever seen and it was a great reward for beating the game. Every time I listen to that song, I feel like playing Okami again... but then I remember that it`s 70-hours long.