Sorry, I'm confused.
You correctly state that suppressing doesn't exclude them from the other totals, and that they should be in the other totals...so why can't you suppress.
The reason that the report runs slowly is that every time a subreport is called, CR opens a new connection the database and pulls the data back out. So a report with 100 employees will hit the database 101 times, which can be significant if there is alot of traffic on the network, the database server, or alot of data is being queried for the subreport.