1. I don't think there are many good open source SFUs to choose from. I know of 2, maybe 3 (including our new one). There may be many, but few have good rate control. But maybe I just don't know about them? I'd be happy to learn of more good ones.
2. Echo cancellation is certainly a hard problem, but it doesn't conflict with E2EE unless you do it on the server, which isn't necessary. So perhaps it may be a somewhat harder problem because you close off one possible approach (doing it server-side), but many (most?) echo cancellation solutions are done client-side.
3. You may not be completely dependent on WebRTC's echo cancellation any more because of the new MediaStreamTrackProcessor and MediaStreamTrackGenerator APIs. I don't know if it will work for echo cancellation, but it might.