No, the Republicans did not break a rule. It turns out, according to Vox,
Wednesday, Republicans deployed a workaround — Republicans on the committee used a "unanimous consent" clause to suspend all of its rules for the meeting, then voted to confirm the nominations for Steven Mnuchin, up for Treasury secretary, and Tom Price, nominated for Health and Human Services secretary.
So because 0 Democrats were there, 100% of the people in the committee agreed to a new rule, to suspend the rules. That suspension meant they no longer needed the quorum to make the appointment.