A more integrated EU would not bode well for Israel. There is by now ample evidence to support the prediction that the more power Brussels has, the more it will abuse it against Israel. This may be seen, for example, from the discriminatory labeling of settlement products and the financial support for extremist so-called humanitarian Israeli NGOs – in reality humanitarian racist bodies – which remain silent about the genocidal intentions of Hamas, the largest Palestinian party. The EU also interferes in the in the Israel-controlled Area C in opposition to Israel’s declared wishes, including financing housing for Palestinians there.This is why a dissolution of the EU would honestly be better for Israel, but not just here: even for the rest of Europe, it would be better, because the EU's proven abusive to the rest of the continent too, and they're one of the reasons jihadists have been able to penetrate so badly into European countries. The subject does come up in the article too. So, that's why I don't think all Europeans would consider it a loss were the EU to dissolve, any more than Israelis would.
Double standards are at the core of anti-Semitism through the centuries. The EU has frequently applied these against Israel. The requirement to label goods from Israeli settlements – something not demanded for areas elsewhere which are similarly in dispute – made the EU bias against Israel so explicit that the Simon Wiesenthal Center gave the EU pride of place in its annual 2015 list of major anti-Semitic slurs.
Besides, the EU's proven itself as corrupt and bad an example as the UN. That's why it's better if the EU goes.