There are lies, damned lies, and Deep State shenanigans.
Mueller is there for a reason, to get Rosenstein to sign off on immunity for Comey and McCabe.
The President need not fire Mueller. He need only have a directive issued and served on Rosenstein that explains that any immunity dealings are subject to presidential review before approval.
If Comey, in the otherwise illegal unmasking activities, was acting under classified directives from the former POTUS, then surely Mueller would want to hide that fact to protect both Obama and his friend Comey.