Have you tried clearing the data for the Phone app under Managing Apps? To get to the Phone app, you need to select "All" in the menu across the top in the Apps settings screen, by swiping left on that top menu area.
I have not tried clearing the data for the phone app myself, so I cannot verify that this will get rid of the frequently called numbers list. But that is one of the places you might try.
Also, there are some "history erasing" apps available that clear history lists. Look for one that works for ICS phone app.