In Joomla! 1.0.x: No
In Joomla! 1.5.x: YES, but with this method only: http://www.dioscouri.com/forum/func,view/catid,4/id,2224/#2219 (special thanks to Renato for implementing this fix to com_wrapper, something we at Dioscouri believe should be part of the core)

The reason this fix is necessary is that other than the `Itemid` value, com_wrapper URLs are all identical. JUGA doesn't distinguish between Site Items based on their `Itemid`, so if the only variance between two menu item links is their Itemid, then JUGA will treat them as the same link.

In other words, you won't be able to get JUGA to distinguish between com_wrapper items, and therefore won't be able to assign them to different groups (unless you're using J! 1.5 and implement Renato's fix).