Generally it's okay to just use the two rails with your isolated converter, however there is a precaution you can take to be sure:
That is to add two Schottky diodes (eg. 1N5819 or the SMT equivalent for a small supply), one across each supply (reverse biased, of course). That ensures that if one supply rail is much stronger than the other and there is a surge from your isolated supply (either at power-up or because the output gets shorted or overloaded) you cannot reverse bias any device that is living off a single supply-to-ground.
For example, suppose you had a single supply op-amp connected between +28 and GND, and your isolated converter drew more than the supplies could deliver (say because some numbskull shorted the output with a test probe). It's possible the +28 could go below ground while the -28 is still supplying a lot of current. That could drive a lot of current through the (now reverse biased) op-amp power pins, possibly destroying it.