I suspect that Moffat didn't figure out what he was doing with season 7 in time for the books to fit between series 6 and 7 (or wasn't willing to tell Justin Richards). With the exception of the first batch in 2008, the books have done a pretty good job of keeping current with the show. If Rory & Amy aren't going to be in the show next year, I can see why BBC Books wouldn't have wanted to develop books featuring them.The puzzle to me, in terms of merchandising, is the scaling back of the novel line in 2012. Yes, we're getting several high-profile books, but the abandonment of the NSA line (as far as we know) is a complete puzzle.
From the Doctor's perspective, there's 200 years between The God Complex and The Wedding of River Song that could be ripe for novels to exploit. Not to mention the undiscolsed period of time between The Wedding of River and The Doctor, the Widow and the Wardrobe. True, he has no companions during this time, but we've had companion-less NSAs before.
In fact, the upcoming Eleventh Doctor "adult hardcover" Dark Horizons makes no mention to Amy and Rory so it seems they may be following this very idea.
Still, I guess you could be right that since they had no idea what was in store for season 7, they may not have wanted to step on Moffat's toes so to speak.