Interestingly, Sullivan's order may actually provide Mueller some cover here. Mueller may have been aware of the illicit FISA surveillance but almost certainly did not use any of it in his investigation. Even if he were rabidly partisan in the case, he would know better than anyone that the evidence was so tainted it would never be admissible in court.
So the only way he could deal with it was to lay low and ignore it until someone else would eventually reveal its existence in a very public manner that would allow him to deal with it as if it were the first time he was "officially" aware of it. I believe this is precisely why the announcement about the delay in Flynn's sentencing was made within 1-2 days of the release of the Nunes/HPSCI memo.
I am not nearly as sure about that as you apparently are. Mueller is obviously a pick from the deep state, and thus most likely felt he could act with impunity, in my opinion. The Nunes memo meant he had to create cover, mainly because he doesn't know how this judge will react to his case.
He is an article regarding the dismissal of the Senator Ted Stevens conviction. Judge Emmet Sullivan is not going to let Mueller skate on violations of Flynn’s constitutional rights. Sullivan is going to rip him a new one.