I think this is kind of braindead. I have several clients with Agile and waterfall teams using the same Jira instance. They want to have only one instance for reporting reasons, so having multiple instances is, at the very least, a hacky workaround, even with Federation. The waterfall teams don't want to know anything about Agile, so why does it make sense that they should be forced to see Greenhopper buttons? Restoring a working "Global" or "Per Project" enabling of Greenhopper is an essential feature.
As Shaun mentioned, we will not be addressing this issue as this is a fundamental part of our functionality.
Regards,
JIRA Agile Team