one way, is to associate a cookie with those users and either a) don t load the tracking code when cookie is present, or b) in Analytics Settings -> Filter Manager, add an exclusion pattern matching the cookie name. a) would be more flexible.
now, there s no way to tell if the user is going to stay on the main site or hop to the client area... so it might undercount in some cases. but you might find that better than the overcount showing up now...
a slightly more intrusive option, would be a JavaScript overlay / splash screen that shows up when you detect a user returning that asks them, "Would you like to go directly to your client area? [YES] [NO, TAKE ME TO THE MAIN SITE]". in that case, the tracking code wouldn t be loaded unless, they say are going to the main site...
if using the filter manager method, you ll want to register the variable like so:
<body onLoad=”javascript:pageTracker._setVar( my_cookie_name_guid )”>