the rules committee absolutely has the ability to take away only the unpledged delegates from the state as a punishment.

 However if there is a revote that the DNC agrees meets their "rules", then it might be a gray area about whether technically there is anything left that justifies the penalty of removing the superdelegates under the rules.  I imagine there is something about conduct detrimental to the party, but that is not the kind of thing you like to invoke.