You could prompt for domains that use more than a small amount - say, 25-100k.
Once they hit that point, show a prompt below the toolbar that shows how much data is being used by the whole domain, in real time and allow it to keep on filling up with data until the user says stop or always allow.
You could continue to allow 5mb for each subdomain, but wait until say, 25mb for the sum(*.domain.tld) before prompting. For example, this would allow {www,mail,docs,plus,???}.google.com to continue as they are now until google.com managed to rack up 25mb worth of data. After which point the user might want to know they're holding on to a fair bit of data for one particular site.
Then again, prompting is really annoying, and most people just click "okay" and without comprehending.
Once they hit that point, show a prompt below the toolbar that shows how much data is being used by the whole domain, in real time and allow it to keep on filling up with data until the user says stop or always allow.