If he really didn't believe in the Council do you think he would have encouraged Molly to turn herself in? Yeah, it was close and political, but in the end Harry and Molly carried the day. What chance would she have had had she decided to run, not just from getting the chop, but from becoming a full blown warlock?
That bit actually has always struck me as a bit odd. He really
doesn't otherwise show signs of trusting the Council/Wardens that much... every time I read that part of PG I'm like "why don't you just confront Molly about it yourself and not tell anyone in the Council"? He could have still taken her as an apprentice.
I guess it's because Harry figured the Gatekeeper really knew what was going on from the beginning. (That's the only reason I can see why Harry seems to think Molly would get caught anyway --
Harry is the Regional Warden Commander for that area, and the Wardens are really really busy. Without the Gatekeeper, there'd be basically zero chance of her getting caught if Harry covered for her.)
he feels like they're bureaucratic jerks who play politics instead of doing real work to help. That, by the way, also seems to match Eb's perspective relatively closely.
Which seems pretty accurate from what we've seen them do.
Look how far the plan in WN got -- and it only got interrupted at all because Madrigal was intentionally taunting Harry into investigating. Something like that is
precisely what the Council ought to be watching for, since they claim authority over all mortal practitioners.
And... they talk a lot about protecting humanity, but don't seem to actually do that much. There were 40 years or so between Kemmler's final death and the Vampire War, and the Wardens didn't manage to catch Grevane, Corpsetaker, etc. despite knowing who they were (Luccio certainly did) - one would think they'd be pretty high priority targets.
And ghouls don't seem to be Accords signatories - why hasn't the Council gone after them and other "unaffiliated" supernatural predators that prey on humanity? The Council's laws clearly don't consider them to be "people", so why aren't they long extinct?