The entire question of criminal charges against a sitting President is surprisingly unsettled: it’s not even clear whether a sitting President can be criminally charged at all, or whether this would violate the separation of powers. Trump certainly seems to believe that the answer is “no,” including for crimes committed before taking office; but as far as I know, no court has ever ruled on this.
It’s not settled, but most jurists agree that you cannot charge a sitting president. The courts would most likely rule in that way, due to the fact that *if* a sitting President CAN be charged, then any group with anything at all could start throwing crap up against the legal wall that the President would have to take time to respond to.
IOW, the courts could be used as an obstruction device against a president with which you disagree. That’s pretty third world.
Mueller charges one or more of Trump’s co-conspirators with a bunch of federal crimes, including conspiracy. If Trump pardons them, he immediately files a new conspiracy charge, now alleging the pardon itself as an overt act.
If it’s ruled you can’t charge a sitting President, then he can’t. Point’s moot. This can all occur, but it has to wait until Trump is out of office.