GroupWise has no way of knowing which ones you wish to keep and which ones are strangers you will never message again. The logic of how Frequent Contacts works would have to change - sort of like prompt you with a dialog box that says "do you want to add this person to your frequent contacts list?".
Here's a way I just came across poking around in my address book. (GW v6.0):
Open the Address book. Right-click on the Frequent Contacts Tab, choose Filtering, choose "Filter for at Least 3 References". I'm guessing this will go a long way toward what you wish to accomplish. In fact I'm going to turn it on in my own account.