And think of how many times it vindicated them. Like I said earlier, we have a thousand years of unknown history here. It's hard to wrap one's head around, but their ways obviously worked out well enough. It might be more crucial than you realize. Human corruption can be combatted any day, but you couldn't go back on a decision like ridding the Seekers. Not easily and/or if the writers insist on it at least.
I can't, though, there's no records or histories available to us, thus no context. Whether or not this is due to their secrecy or a lack of events as significant as the most recent one is anyone's guess. All we know is Cassandra stating that at some point, they turned from their original endeavor, and during the most recent crisis where their skills and judgement were needed the most, they instead chose to help set Thedas ablaze.
I understand. I haven't figured out the problem myself (checks and balances). I've been thinking about it even before the game came out. Cassandra hasn't quite figured it out either (or rather, Gaider doesn't want to get into it yet). All I know is that it's a problem to be solved. I'd rather look at it like a scientific or math problem. Sit around long enough or hash it out with the right people, and you can come up with solutions. Ridding myself of them however is not my idea of problem solving.
From that perspective, my view is that the Seekers represent an additional problem to be worked through, rather than a definitive solution to the more important one. To make things worse, Cassandra herself doesn't even seem to be trying to solve the right problem.
She expresses a desire to do "the Maker's work, in truth" and yet can't decide what that even is when pressed. But the Seeker's aren't supposed to be about figuring out what the true nature of "Maker's work". Their raison d'etre should be simple: to hold the Circle together and ensure protection unto the Maker's believers, with the problem solving being based on how to best do this. If we can't even be on the same page when it comes to that, I'm afraid even Cassandra might not be able to really fix the Seekers.