soulgrindr: Nah. They already had a non-commercial contract with them. That meant they had a fair bit of control.
Activision could even have worked out some kind of deal where the game carried free advertising for their products. The same way valve exploit their fan's creative energies to create word of mouth for TF2 or whatever.
There wasn't really anything for activision to lose, and if they played it smart there was a lot to gain. Heck, they could even set up a "fan projects" section of their website and milk the good will and publicity.
Unless the fan-remake sucked. Or, more likely, was faithful (which, for most people these days, would mean "sucked").
Free advertising? Look what happened when Far Cry was free with a bunch of McDonald's ads. People got annoyed.
And there is always something to lose: If they ever want to make their own game with the IP (unlikely, but whatever), there is the massive threat of "Well, these guys did better. And it was free", which will smack the crap out of sales. And even if it wasn't better, people will see "free", try it, get disappointed, and never try the completely unrelated remake :p
Milk up the publicity and good will? Didn't Infinity Ward actually donate to charity as a promo for people playing Modern Warfare 2? Didn't these very forums get angry and scream about how they are horrible people and shouldn't be doing that?
Yeah, Activision is going to benefit from trying to profit off of fanmade remakes of IPs that a lot of people probably already feel they shouldn't own...