The constant requirement to toe the Chantry line is irksome. My latest play through my elven Inquisitor at every opportunity has denied faith in the Maker, refused to accept the title of Herald and wanted people to know the truth about how he came by his mark but is continually ignored or patted on the head and told it is best to leave the people to their faith. This doesn't even just come from Chantry stalwarts like Cassandra, Leliana or Mother Giselle but even Hawke urges him to keep quiet about it. By contrast, when they discover something about his People's traditions and gods everyone seems only too glad to dish the dirt. When to my mind the Dalish got an awful lot about their past right, whereas everything that has been revealed about the Chantry and the Maker points to their religion being a big fraud. (WoT2 was a big eye opener but I do also wonder where the Maker was when Solas raised the Veil).
However, back to the main point of my post. The capacity for evil decisions was watered down from what we were shown in early extracts from the game. Nevertheless a remnant does still exist as shown in the Keep options. However, it would seem that in terms of the reaction to the Inquisition 2 years down the line, it makes no difference if you were a committed follower of the Maker and a paragon of virtue, or a Maker denying evil bastard (not closing the rift at Crestwood when you have the ability to do so does seem to qualify in my mind).
What would have been interesting and made sense would be that if you had been claiming to be the chosen of the Maker, people had found out the truth and that was the reason they turned against you; which I would have found both plausible and more acceptable than simply I'd stayed in a vacant Keep a bit too long. Then reducing the size of your Inquisition and putting it under the control of the Divine would have been your face saving and long term survival way out of it.
By contrast, if you had been denying faith in the Maker and chosen status, this would also have been leaked and thus the faithful would no longer believe in you, again giving a plausible reason why you had no choice but to disband because you no longer had the support of the common people, let alone the nobility.
Currently it makes no sense with such a major threat as Solas having been identified to reduce the Inquisition in size if you are going to retain it. If the organisation is riddled with double agents that is going to be the case no matter how big it is. The simple answer (not one that I like advocating but there none the less) would be to purge it of all elves. Since we are told at the end they run off to join Solas anyway, we don't actually have to do much to achieve this. No matter how corrupt and self seeking the other members of the Inquisition might be, it is not in anyone's interests that Solas should succeed in his plans since he has admitted we will all be destroyed. Even qunari agents should be aware of that fact. So keeping our current network of spies throughout southern Thedas (and even to some extent in Tevinter) with a force sizeable enough to take action wherever it is required would seem to make sense to me. That is not what I understood to be function of the Divine's peacekeeping force since the majority of the army is disbanded regardless.
My elf disbands because he still retains his cultural belief that he should submit to no one, least of all the Chantry, which is what the Divine represents. He wants to focus on one thing alone, the hunt for Solas. He always knew the humans would turn on him in the end. He had the example of Ameridan to show how he is likely to be wiped from history and end up being depicted as a faithful human but at least this way may be some people will remember that he didn't willingly merge his organisation with the Chantry. I was happy to go with this because I saw the Inquisition as an independent organisation that stood for all and if it can't be that way and continue, then so be it.