I've been wondering myself. The obvious answer is that he wanted to protect konoha by keeping an eye on the organization.
However, being in the organization he'd have to help them get the tailed beast, but if he wants to protect konoha he can't capture Naruto, so he'd have to go easy on them. But then wouldn't the organization know he was holding back? And then question his loyalty? Idk all the answers myself...
The only thing I can really think of the akatsuki in regard to sasuke, is just to fuel his growth.