In Edit Preferences, give the registered user an option to hide certain fora (or alternately, have the user Subscribe to only the fora s/he wants rather like in a Usenet reader).
I think it might get confusing if Mark All Forums Read didn't mark all of them to the same timestamp.
But I agree that it might be a hassle if you've taken the trouble to hide a forum with an infinity+1 stamp to have to do that again. And since at present the only way to hide a forum is with an infinity+1 stamp, it's probably simpler to add a condition to Mark All than to implement something in EP.
Cheers,
Scott.