Are you installing to the same bottle? I imagine that you're using the Install Unsupported Software button in CrossOver's Software Installer. CrossOver then warns you that unsupported software may break things in an existing bottle and so warns you to create a new bottle. However, in this case that would be wrong. You need to install into the same bottle as CoD2 so that the patcher sees the game.
If that wasn't the problem, then I'm not sure what's going wrong. As you guess, it may be failing to find a registry key. It might also be failing to find a file.
Did you install CoD2 using version 7.1.1 of CrossOver Games or did you install it with an earlier version and subsequently upgrade? If the latter, it's possible that the earlier installation was incomplete and that a new installation would be more complete if some bug was fixed in CrossOver Games in the interim. It might be worth trying to install CoD2 into a new bottle and then patching that. (It might also work to just reinstall CoD2 into the existing bottle to see if that fixes whatever the patcher is looking for, but that runs the risk of breaking CoD2 and losing saved games or whatever. Archiving your working bottle is an alternative way to protect yourself against that risk.)