I’ve never heard Gilmour speak about it, but maybe I missed it. I would be surprised if he were on the same side as Waters on this issue. He seems to have better sense and much more class.
Waters isn’t the only member of PF whose brain is comfortably numb.
http://www.stereogum.com/1903731/pink-floyd-reunite-to-denounce-israel-in-statement/news/
Gilmour certainly has more class than Waters (and he’s long been one of my favorite guitarists), but he’s very deluded on this issue.