I don't think we ever saw the head of THRUSH, just the THRUSH agent of the week. Although there was one where they captured the third man from the top, I think it was.
Although of course a movie would do things differently, so they could give it a head.
And Cruise is playing the hero because they want to attract the Mission: Impossible
movie audience. I doubt that The Man from U.N.C.L.E.
has enough name recognition today to rely on that alone, so they want star power and some coattails to ride.