For isolated designs, I usually connect the ground from one side to the Spice ground, then the ground from the other side to the Spice ground through some high-value resistor, typically > 100 Meg.
There's no way around it, Spice needs a single reference node.
The high-impedance-between-grounds "trick" is not just a trick though - it actually models reality. Infinite impedance is just an ideal situation that you will never encounter in real life.
You can of course model your isolation with some impedance that's more sophisticated than just a resistor, depending on what you want to simulate and the kind of isolation you're going to deal with.