As I understand it...
The Freys got Riverrun after the Red Wedding. The Lannisters, Freys, and Boltons were all working together against the Starks and Tullys so I believe this is sort of just an extension of that, they want to give it back to the Freys so that everything is back as they had planned post-Red Wedding. Of course they're going to have much bigger problems with the Boltons in the north soon enough!