Here's the result after adding a 0.1uF film cap in parallel with the pump. I got the cap from Radio Shack.
With the cap installed, the worst case dip in the 12V rail was to about 9.5 Volts. Not great, but vastly better than without the cap. As long as you don't share the drive cable with other devices, the PSU's output caps will filter this enough to keep the rest of your hardware happy. Radio Shack sells these capacitors in two-packs. It wouldn't hurt to use both in parallel with the pump, although it probably won't reduce the remaining spike by a factor of two.
Edit: Also, with the cap installed, there is no need for the diode. The diode would have prevented any spikes from getting lower than -0.7 Volts. The capacitor alone is sufficient to do that.