The fact that Hashem gave us Yerushalayim and the Kotel is a great gift. Yes, some people don’t treat it properly, but that doesn’t take away from the gift we received, and doesn’t take away from the hakaras hatov we must have.
It’s like the government funding yeshivos. Sometimes we hear that people affiliated with a yeshiva got in trouble for stealing funds. It creates a chillul Hashem. Does that mean we should be against the government for funding the yeshivos? Obviously not!
Let’s look at the good that Hashem gave us. If you have issues with the actions of some people, take it up with them. Don’t lose the appreciation of the gift from Hashem.
Mods: regarding the Har HaBayis, yes, most chareidi Rabbonim hold it’s absolutely forbidden. But there are some who hold there are certain areas we may go to (such as R’ Tendler). I’m not endorsing or attacking those opinions. It’s never been a question for me, so I never asked my Rav what he holds. But if ymbyi is a follower of a Rav who holds it’s allowed, then there is nothing wrong with him following that psak. If I was going to Israel and wanted to go onto the Har HaBayis, I’d ask my Rav what he holds, and would follow what he told me.