Yes, I can see what you mean. I think that the moment in X2 where Erik tries to kill the entire human race (using Charles and his mutation, no less) was one of the worst things Erik ever did. You can understand why he might have lashed out in anger when he discovered what Stryker was planning, and I think to him it would seem fair to turn the weapons of the humans against them. But, this does not excuse the callous way in which he approached mass genocide. It’s an understandable reaction from someone who has been terribly abused, but that doesn’t mean it isn’t morally reprehensible.
Regarding Erik as a metaphor for Israel, I think this is a difficult issue. There’s a very good discussion of this concept by a Jewish journalist here, and another article with a more Israel-critical stance here. Personally, I see Erik’s terrorism as an attempt to liberate oppressed people (mutants) from an overwhelmingly oppressive majority populace (humans). But Israeli aggression against Palestine does not have the same clear imbalance of power. If anything, I think Palestinian people are the opposed group and the state of Israel (NOT all Jewish people, but the specific state apparatus) is the oppressive force.
I see Erik as more analogous to violent left-wing extremists like the Baader-Meinhof Group, or eco-terrorists. Their aims are promoting socialist, humanist values, such as freedom from government oppression, anti-imperialism, and the protection of vulnerable groups. But the methods used to achieve these aims are clearly anti-humanist, promoting violence even against innocent bystanders. This is what makes Erik so polarising in fandom, I think - his intentions are good but
his methods are inexcusable.