You have to ground to earth the equipment (case) by regulation, even if the 3 phase power is without neutral. (is the neutral of the main transformer isolated, or just the power cable have only 3 wires?)
You can still conect your minus from the 5 v power supply to this ground, and add a second 24 V ac transformer for the digital input power supply. The idea is to separate the (presumed) long cables of the digital input from your logic, and to conect them only in one point that is conected also to the ground. The voltage of the equipment conected to earth is low (below 24V) and it depends from EC standards if it's OK or not.