A lot of the criticism of 40k comes from our perspectives though. The Inquisition aren't powerful. They don't maintain massive fleets or armies, they have specific forces useful for particular things, but they rely extensively on others to do what they say.
The Inquisition rely instead on relationships and mystique. They understand this:
"I carry with me an Inquisitorial Seal. It is a small, unassuming object contained in a neat box of Pluvian obsidian. It is a modest thing, relatively plain, adorned with a single motif and a simple motto. Yet with this little object I can sign the death warrant of an entire world and consign a billion souls to Oblivion."
For their operations to be successful it's absolutely essential that people listen to them and don't question them. The Lions questioned an exterminatus and then went round for 50 years bugging people about it and complaining to various people. It was essential for the Inquisition to crush this dissent because if it wasn't then they'd have continued disobedience from other chapters. As soon as people start thinking they can stand up to the Inquisition the whole affair comes crumbling down.
The Inquisition would have to start being more overt, trailing around with fleets after them or large formations. The whole purpose of them relies on them being relatively quiet for a long time, then jumping out and ordering stuff to happen, which questions from others would delay. For example, say a Malleus inquisitor knows about a daemon summoning on a planet that's otherwise peaceful. The Governor and other authorities are complicit, and the Inquisitor requires some passing fleet to fire on the planet to prevent a disaster. Then the fleet just says 'I don't see any corruption are you sure, I'm not going to attack them'. The daemon gets summoned, various bad things happen.
The strength of the inquisition is in their navigation of the weird feudal system of parcelised sovereignty that the Imperium operates on. If they can't do that they might as well be some random arm of the Adeptus Terra.
Just as a final edit: IMO the Lions were the guilty party here. They threatened the entire system of the Inquisition and the functioning of thousands of operations across the Galaxy. The Inquisition were entirely justified from their perspective, and even from other chapters like Grimaldus. That doesn't mean the Inquisition's actions were necessarily morally correct, or that they couldn't do something else, but within the logic of 40k they were justified.