Thinset is actually an adhesive, whereas grout is not. I would guess your seams will fail over time. If you cover up the wall with a good membrane system (I use Kerdi) you will make it moisture-proof, but the mechanical integrity of the underlying wall structure won't be what it should be. All in all, treat the wall as though you had never seamed them.
If you installed the cement board with screws (you DID use screws, I hope), just take out the screws, give the board a little shake, and the seams will fall apart. Brush off the grout with a wire brush (or probably even a stiff scrub brush), screw the board back up, and do the seams again the right way.