Its even simpler than that. Mark had to pull back because he didn't want to publicly want something that hasn't been (or will ever be) worked out yet between studios. Your right, IMO about the bad press though but Just like the Producers (Arad,Donner,etc) can wish but have no say of what crossovers happen or don't happen. And, all they've done is made the natives restless for some type of wider shared universe. Mark Millar can only work the magic depending on the size of the stage his employers allow. So for now he can only advise to make it tone wise cohesive with the Disney and Sony Marvel Universes.
Plus I don't credit any fans for him getting the job. Just like he said that he was apart of the Ultimates (Avengers) and made that known though the introduction to the Fox execs from Joe Carnahan and the Marvel movie Avengers was based on the Ultimates more than 616 continuity. They saw him as a link that could bring that tonal feel from the Avengers to their Marvel properties so, good or bad they were looking for a way to clone that success with in their Marvel films through him.