Then Let Trump Pardon Flynn, that way all the evidence comes out. People are objecting to the Justice Department under Barr- which is supposed to be politically neutral - interfering after Flynn admitted lying to the FBI twice. If Trump were to pardon him afterwards then the public would learn what he was trying to hide. (There is a reason he lied you know). Barr's intervention conveniently hides any damning facts, so it's covering Trump's ass.
The two situations are different. Now, if the process continued and Flynn was convicted and sentenced, and the public learned of all the details, and THEN Trump pardoned him and peopled complained, then you could say it was hypocritical. Right now, there as never been anything like this in American history with the Justice Department acting like Trump's personal political ally.