It is currently possible to restrict groups from being refreshed during "Refresh all groups".
However to disable a group, this must be set individually for each group in the Download Settings page of the group.
This is a PITA if you want to say, disable all groups except a couple and you have 30+ groups.
A solution might be a pop-up screen accessible from say File-->Options-->Refresh Groups which would display a tick box list of all groups where you can 'select all' and then just untick the groups you want refreshed. Or vice versa.
Cheers,
Wilson.