I don't see an issue, as long as they don't use props, costumes, or "delta" insignias from JJ's Trek. An alternate universe is fine, so long as it isn't JJ's "alternate" universe.
Well there is the fact that they might be using a similar bridge to the Kelvin if the facebook photos are to be believed.
I don't see how having a bridge similar to the Kelvin would be an issue. Only way it would be an issue would be if it was 100% accurate to the one used in the 2009 movie, which I highly doubt would be possible. As long as they don't use the actual ships from the 2009 movie, or any of the costumes, props, or storylines (no references to Nero, and not set an the alternate universe), I don't see an issue.
I don't have any problem with the production itself, this is more of a theoretical question - if we know now that Paramount doesn't want anything from the 2009 film being used in fan films, why test their patience with us by hewing close to it at all? Then again, it is entirely possible the guys at Star Trek Begins don't know about the restrictions Patty shared with us, so it's a moot point. I'm just thinking out loud.