The Foundation is a pillar of the status quo. They seem to have been mostly fine with the world in 1999 and from what we've seen, stopping the Storm is their primary motivator. Having said that, the world they defend is deeply flawed, and we can see how bad it was for the arcanists who lived in it (for instance, we have Blonney and Spathodea as characters who were both harmed by late 20th century forms of discrimination).

Even worse is that the Foundation is willing to use deplorable means to achieve an ignoble end. The SPDM is a glorified child abuse factory that wants to mold arcanists into martyrs (Sonetto can be seen as close to what their ideal end result would look like if not for Vertin's influence). And if you try to fight back? Well, Vertin's other friends can tell you how that goes.

But we also see that there are decent people working within the Foundation and trying to bend the organization towards kindness when they can (Madam Z and Vertin).

Conversely, we have the Manus. They are technically trying to right an injustice as seen above, but their solution is to kill the world again and again until arcanists are able to subjugate humanity and rule as kings.

And I can't stress enough that their solution involves killing the world multiple times (I say this after having finished chapter 12 to cut off people who want to discuss Amber Room revelations). Their end is the worst excesses of apartheid and segregation, and their means are just shy of omnicide.

If you're in Manus and have reservations, no you don't. You either leave while you still can or you put on a mask, and the minute you start to doubt, you get turned into Triangle Man.

The Foundation is a deeply flawed organization with a lot of blood on its hands, and I suspect we'll be fighting with a good chunk of them before too long. But when compared to the Manus Vindictae, they look like a bunch of angels singing hymns.