If you do not ground the secondary of a transformer, then a single ground fault on the secondary side will not trip an OCPD. While ungrounded systems are intentionally used to provide continuity of service in case of a ground fault, I don't believe that this is applicable in your situation. The secondary of your 480V to 240V transformer needs to be grounded.
The question remains open as to _which_ terminal to ground. Common practise would be to ground the neutral of the secondary, giving a common 120/240V system. You would use normal 120/240V breakers, and your heaters would be served by double pole breakers.
As I stated above, I believe that you could ground one of the 240V terminals, and simply have a straight 240V system. This would be a 240V grounded system where one of the circuit conductors was a grounded conductor, and the other was the 'hot' conductor.
Additionally, for 2 wire to 2 wire transformers, the secondary current is a direct function of the primary current, and you may be able to rely on primary OCPD only for all of the overcurrent protection. It isn't a given that this would work (for example, if the OCPD required for proper secondary side protection is too small to prevent tripping on inrush), but if it does work this could make the installation much simpler.
What size transformer are we talking, and how many watts of heat?
-Jon