Create a self relationship between Site::SiteActiveFlag. Then use this table occurance in your count calculation.
Since you have a filtered portal, define a summary field in your portal's table that is the "count of" some never empty field in the table.
Place this summary field inside a one row portal with the same portal filter and it will count the number of records showing in the filtered portal.
Please note that this is a "read only" way to get summary data from your set of records shown in a filtered portal. You still need to use S Chamblee's approach if you intend to create calculation expressions that must refer to this summary data.
Many thanks both, I only needed a 'read only' figure so Phil's method worked fine for me this time. I'll experiment with S Chamblee's suggestion as well though :)