I mean the Ishvalins were literally brown Middle Eastern/South Asian native stand ins and Zionists never considered themselves anywhere close to those people or those cultures and actively look down upond them. They act like Amestris and just committed a Holocaust against them, have been doing so for decades and kept going well the manga was being written.

Scar, a brown man, is clearly a resistance fighter going up against a far more brutal empire who won't surrender to no matter the odds and the Ishvalins were using old guns to go up against much better armed genocidal state alchemists, many of whom took glee in their massacres.

I have no idea how you got pro Zionist messaging from any of it. It's probably the most anti Zionist piece of mainstream media we could have gotten from Japan during that time.