Hi Alphalegacy,
I had the exact same issue as you (http://www.bikeforums.net/showthread.php?t=365456). And the answer,fortunately, is yes, you'll be fine. I'm not guaranteeing anything, but chances are the trainer will have clamps that hold on to your axle just like they'd hold onto the ends of a QR skewer.

P.S. I'm using the Minoura RDA 850 rim-drive trainer.

Good luck!