Obligatory mentioning of Apolytons source code project:
The source code of CtP2 has been released somewhere in the past and the community of Apolyton is working on understanding and improving on it. More info on http://ctp2files.apolyton.net/source/. I guess the gog-version is compatible with it.

There's a certain quote from the FAQ troubling me...
"the data and media files are not included in the source code file, so you still need to buy a copy of the CD to be able to use the code. Also, in the EULA (user agreement) is set up in such a way that changing the game so that the original game is no longer needed to be able play is strictly forbidden (this means no no-cd patches). Basically, we may edit the game as we see fit, as long as resulting updates/new products still requires the CtP2 CD to play"
Thus I'm afraid patching the GOG version will restore the CD check. Very-very afraid.
Hope there is some kind of solution possible, since the community patch sounds beyond fantastic.
edit: Those curious should track this thread:
http://apolyton.net/forums/showthread.php?t=190347

Well, I'm gonna try it now anyway

Think the exe will change.
Look forward to your results, though.

Well, the program itself starts fine, but when you 'launch' a new game it indeed asks for the CtP2 cd. Too bad, I'm not going to play CtP2 without the community patch, so I hope Activision will grant a no-cd check to Apolyton.
EDIT: Or you download the source-code of the latest edition and remove the cd-check yourself. People over at Apolyton could help you with that, they just can't release as such.

Guess our best bet is that GOG compiles an EXE for us and makes it available through game extras...

I hope they get rid of the popup windows and display information on the side of the screen like Civilization.

Update on the story:
"I simply trust my interpretation, not releasing a no-CD version simply harms now Activision. So I have to release it as soon as possible, preferably today. But my time is limited and I have some more fixed in the pipe that should also be tested a little bit more. Well, but this shouldn't take to long."
So hats off to the maintainers of the project!
Update 2:
Version of 2010 Feb 28 is GOG-Compatible.

And I can confirm it works.

Good to know. I'll suspend my vanilla game and throw myself into the apolyton version.