I don't know how we missed it, but Gmail+Growl stayed right in stride and released a 2.0 version to work with the new Google Notifier (in which case, shouldn't this be called Google+Growl?).
As long as you shut off the built-in alert system in Google Notifier, Gmail+Growl works well with the new utility. The one quirk I've found so far is that it doesn't seem to be pulling images from Address Book, and I don't know if this is a problem on my end or an update is in order. Either way, if you prefer Growl for all your system notification needs, Gmail+Growl should fit the bill just fine.