I may be wrong, but I think you misunderstood the 'stripping the messenger app' bit. It's not referring to the web app, just the ios app. Facebook stripped the messenger app from the main iPhone app a few months ago. I don't think there are any additional TOS.
Messaging is definitely still in the main iOS app. They advertise "The new Messenger" with banners to get you to switch, but I haven't bothered.
I tried it out briefly, and IIRC had some trouble with chat notifications still coming from the main Facebook app. I could turn off notifications for it, but that'd kill all of the other notifications too. Making chat only in Messenger would solve this, if they haven't fixed it already.
Just tried again, it looks like once you have Messenger installed it gets disabled in the main app. And this time my message notifications are coming from the actual app that I can read messages in, so I'll stick with it.