Sure, that's a big issue. But it might not be as bad as it seems. The reason a native Gmail app is such great news is because of the special way in which we read and organize our Gmail accounts: Priority Inbox, tags rather than folders, stars, etc.

There will probably be nothing special about the native app's compose interface, though, so I don't see that it will be a problem to keep the account registered in both clients, but only to sync regularly with the native Gmail app, and to use whatever app iOS picks (undoubtedly MobileMail.app) when composing.