User blog comment:AYET/More about chapter 700/@comment-4899461-20130301053743

It seems as though no matter what, the government just wants to keep the world powers in balance. The Shicibukai exist to help the government maintain balance. Mangastream's (though not the more reliable mangarule's) translation also suggests that the marines are aware that the Shichibukai mostly serve a symbolic role, and are not necessarily trusted as true allies. Plus, based on the actions of the World Government in the past, I would think they would choose losing one Vice Admiral (pre-skip Commodore) over losing one Shichibukai, because the loss of one VA isn't going to throw off the world's balance.

Also, while we don't know if the government knows about what Law has truly done or not, I think it's safe to assume that they would be way more pissed at Law for finding out he made them lose Doflamingo than they would be at him for allying with Luffy.