Everything McRaven wrote about Brennan can be true, and it can still be true that Brennan deserved to have his clearance revoked. Whatever his alleged integrity, Brennan was caught in several high-profile lies and obfuscations (regarding: the CIA's illegal access of Senate computers, the CIA's illegal acquisition of other protected communications, the allegation of zero drone strike collateral casualties, denial of knowledge of the Steele dossier).
In the previous administration, Brennan (Dir CIA), Comey (Dir FBI), and Clapper (Dir NI) were significant players in the US defense/security establishment responsible for preventing things like foreign interference with US elections. It has been established beyond doubt that the Obama administration knew about the (Russian) attempts but did not pursue the matter as aggressively as it might have. Whether the directors' hands were tied in their respective areas of authority by the administration is almost beside the point; the customary principle is that if you can't get behind a policy, you should resign. So presumably they "got behind" the policy. Nevertheless, there was a failure on "their watch". If they have useful advice to offer, it is the sort of thing done quietly through established channels. Carping openly serves no agenda but destabilizing the new administration. If they wish to be critics or to pin blame, they surely have a right to do so - but they do not necessarily deserve special access.
Here is what revoking the clearance really does: prevents anyone from sharing (leaking) classified material with Brennan without risk of committing a felony. It discourages leakers inside from using Brennan as a delivery conduit.