Okay.
Great that the mod made it to slashdot.
Bad if we have copyright issues.
Assuming that this is the case (doomsayer that I am), there's one direction to go.
The way I see it, we're dealing with the portion concerning mods in Vegastrike's GNU license here, which reads:
2 b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
part thereof, to be licensed as a whole at no charge to all third
parties under the terms of this License.
So we do have a legal document the can be referred to as basis for negotiations with EA people. As this isn't new, somebody around here might be experienced in handling copyright discussions with EA.
Since PR does not steal code from EA, or hide its intentions at being a remake, or infringes sales on copyrighted EA products in any way (at least none that I know), we have a pretty sound case here.
I guess the UE/Standoff team might have some hints for that (although I'm not clear on the legal status of those mods).
If this doesn't lead anywhere, I'm sure that the CIC staff has good contacts to EA people; and I'm pretty sure there's already communication going on outside this forum to solve possible issues or misunderstandings.
Another good step might be to issue a legal disclaimer on the webpage, stating the intent and legal status of the project. A good example might be the disclaimer from the King's Quest Remake by AGD:
http://www.agdinteractive.com/legal.php (although I have no idea if the same situation applies)
Soooooo, people, don't cry wolf or push the eject button yet. This is a serious topic, but there are plenty of opportunities to solve it.
And maybe I'm too much the pessimist after all, and everything's fine already. I hope it is.