These agencies used fronts to donate money to cold war cultural institutions. I think your speculation is entirely possible, even though it sounds tinfoil-hattish now.

The Cold War example that comes to mind is Partisan Review, a broadly left-oriented journal that published Susan Sontag's "Notes on Camp" and Clement Greenberg's highly influential art essays (http://en.wikipedia.org/wiki/Partisan_Review#Funding_by_the_...), which (it was later found) accepted multiple donations from CIA fronts.

As time went on, some viewed these donations as a tool these agencies found to bolster the intellectual stature of the "New York School" of heroic AbEx painters versus their Soviet counterparts (http://en.wikipedia.org/wiki/Abstract_expressionism#Abstract...).