1) Yes, they did have Morocco stand in for Israel season six when Saul goes to the West Bank. The last time they filmed in Israel was early summer 2012 when they filmed Tel Aviv for Beirut for 2.01 and 2.02.
2) I don’t think you’re a worry wart. That kind of thing just has to be taken into account. On Monday I was looking at a map of Israel as I was reading the news about the protests, and I saw Abu Ghosh on the map. I recognized the name because it was where they filmed some of the opening scenes from the pilot. It’s just 10 kilometers from Jerusalem. It seemed really hard to imagine them filming there today, in 2018.