Without knowing
any of the facts, I can only speculate. But if Smith got the old SIGs in exchange when they sold NCHP the M&P357 guns, those used SIGs are probably worth more than the used M&P357s that SIG will now get in trade. Add to that the actual increased price of a SIG over an M&P and it's not hard to understand how the deal, overall, could be a lot more expensive.
As for other motives, I can't speak for SIG but I'd be pretty surprised if anyone there was taking a "toldyaso!" hard line. Getting a state agency to adopt your gun is a big deal. Getting them to come back to you after ditching your gun is much, much bigger. I'd imagine everyone at SIG knows it's very much in their best interest to recover NCHP as a customer. That doesn't mean they will give away guns for free, but I bet it is keeping the price down even if it doesn't appear that way to outside observers.
Or, I could be completely wrong.