Sadly The Digital Bits must have misread their source. According to the Hollywood Reporter article they link to:
"The agreement excludes about 100 cornerstone Paramount titles, including the Transformers, Star Trek
and Indiana Jones
The original press release concurs: http://www.deadline.com/2012/10/warn...ribution-deal/
It's certainly possible that a re-release of the Trek movies will come next year, either in time for the new film's theatrical or home video release, but it will be from Paramount itself rather than Warner.
There's also a major documentary on the movies that is currently homeless, called "Star Trek Motion Pictures: Beyond the Final Frontier" from King Media Services. I wrote to them a couple of years ago when they had a trailer for it on their site, and I was told they were trying to work out a deal with Paramount. They didn't say what venue it was commissioned for.
So between that and the arguable need to remaster several of the films and release the director's editions of 1, 2, and 6, there's certainly an argument for a re-release. Hopefully it eventuates.