The Court is not obligated to accept a plea deal like Flynn's. Judge Sullivan could have tossed the guilty plea and indictment, or he could have imposed a sentence consistent with sentencing guidelines that differs from what thee parties propose. Jared Fogle -- the former Subway pitchman -- is a perfect example. He was charged with child molestation and possessing kiddie porn. He pleaded guilty, with the deal being that the government would request no more than 12 years and Fogle would seek no less than 5 years. The judge gave him 15.6 years, which was well within her right.
One problem with courts not accepting plea deals is that it discourages plea deals. Fogle, for example, may very well have chosen to roll the dice at trial had he known that the Court was going to stick it to him.
In this case, Judge Sullivan hasn't done anything yet. He expressed an opinion and hinted that he is considering prison time, the government's recommendation notwithstanding. Judge Sullivan hinted it might be in Flynn's interest to conclude his required cooperation before he is sentenced. While it didn't come out clearly, I think that Flynn's comments in his memo to the effect that the FBI entrapped him and tricked him into lying, without a lawyer being present, backfired. Judge Sullivan commented that blaming the FBI wasn't consistent with accepting responsibility. I would never have taken that approach.
Judge Sullivan is no "disgrace." He is a federal judge doing his job.