A jailbreak app making it to the app store being bad, and "apple's walled gardens are bad", are fundamentally incompatible.
They should also provide a way to downgrade iOS via Xcode for those with a dev account, but that's another story.
My MacBook runs homebrew which currently lists 84 packages installed plus their dependencies, very few of which will have been professionally vetted, and of the 127 apps in my /Applications folder only a third of them came from the Mac App Store, and I would estimate that a quarter of the others aren't even signed with a paid developer certificate.
I want the apps that I get from Apple directly to be safe. I want to know that when I put my faith in the App Store that I'm not lulling myself into a false sense of security. I want my parents and girlfriend, who are not technical people, to have that same sense of security without them having to learn entire programming languages to vet source code themselves.
The benefits of closed systems don't go away just because you say so.
App Store policies are a poor replacement for collective action, of course, but let's not pretend we can just become immune to hostile by sheer force of will.