Well, you can start by requiring the extensions to actually request all the permissions they use. Chrome does that now but has very coarse-grained permissions which makes it easier to hide malicious behavior, and in this case the permissions just weren't working so you could do something bad without the permission. The way extension permissions work in Chrome also means that extensions tend to request permissions they don't currently use, which means they can quietly pick up nasty behavior later on.

In the end an extension like Greasemonkey is implicitly unsafe because it's designed to run third-party content. You can't really fix that at an extension store/distribution platform level - so you put that dangerous footgun behind a permission and make sure users know what they're in for when installing it. I'm not sure what else you could really do since greasemonkey scripts rely on the ability to muck with page content.