I don't think the counter ion has much of an effect on the E/Z ratio of WH. More likely its due to the fact that your nitrile which provides the "bulk" to push the stereochemistry is gamma to the phosphonate as opposed to the traditional beta position of carbonyls ect.
Might be able to get away with a lower pH, but will probably have to go with a column (maybe more than one knowing Sn). Fe/HCl reduction might be a viable alternative, and workup is traditionally much easier.