Actually I disagree. If you muffle the toms, you'll end up killing ANY resonance or tone the drums have, that way, it's just as good as hitting cardboard boxes. And like you've mentioned, the balance. The mic will definitely not pick up the muffled drums.
Unless you're talking about micing each drum individually or as a pair, in such close micing situations, yes, muffle them.
Otherwise, just let everything ring out. I think what you're looking for, turbochicken, are thick heads like pinstripes, those should give a nice balance of cut and 'deadness'.
I could be wrong though, as I'm speaking from my own personal experience. Just experiment with various stuff.