Something similar to how Stannis deals with the Karstarks – arrest the lords and use them as hostages to keep the common men in check.
But that’s just a start. Remember, the Frey armies aren’t in the Twins, but Robb has 400 men garrisoning the Twins to keep Walder in check. I’d wait for him to cause a fuss, and then have him arrested for treason against his liege lord, Edmure Tully, for attempting to desert during the middle of a war. (Remember, regardless of how Walder feels about Robb, he owes military service to House Tully and has conspicuously and repeatedly failed to make good on his obligation)
Then, I’d dangle the offer of which Frey gets to replace Walder in front of the lords in custody to divide them and rule.