By asking Flynn if he wanted to proceed to sentencing, he was telling him that he would get more credit for cooperating, and likely a lesser sentence, if he waited until after Flynn had fully cooperated per his deal. That is hardly unfair; ion fact, it's cutting Flynn a break.
As for the treason comment -- eh. He took it back. Treason potentially is a capital offense, but we're talking about 0 - 6 months in federal prison here.