To be safe, i'd connect a load to the un-used channel. Since you're not going to send a signal to that channel, the load could even be a loudspeaker. Safe beats the heck outta sorry.
The danger comes from driving an output transformer's primary when the secondary is open/not connected to a load. Induction can cause dangerous levels of voltage to build up in the secondary winding until it finds somewhere to arc over to a ground, usually through a weak point in the insulation to the core or the primary. Either way, at that point you're in the search for a replacement transformer and whatever else the event took out back upstream.