John Brennan has repeatedly lied to Congress (specifically the Senate). He oversaw the CIA when it engaged in torture. He did not reign in the CIA's repeated flouting of the existing (itself wildly over permissive law regarding securing data on citizens communications). And, he most notably denied the claim - since proved to be true by his own Inspector General that the CIA submitted false claims against the Senate Staff while itself it was hacking into the Senate staff computer.
That Obama seeks to protect his choice is perhaps natural given their long relationship but indulging lawless behavior has its own consequences (and this from a former constitutional law professor who should know something about the rule of law).