My understanding (and please correct me if I'm wrong) is that an 'upgrade' is really a fresh installation, with your user data migrated across afterwards. In that context it's not really a 'removal' as such -- and it's hard to see how else they'd do it.

I'm actually glad they made this change. In the past, XQuartz was sometimes ahead of the officially distributed version, which could be messy. Now they're the same thing.