The difference is intent: It is perfectly fine to have an HQ in a city that is clearly marked as such. Israel placed their intelligence headquarters in the center of Tel Aviv just like any other government building, similar to how for example the MI6 building is in central London, the BND is in central Berlin, DGSE in central Paris, etc. It makes sense to have buildings belonging to a vital government agency within short distance of other government buildings in the capital, for very obvious reasons. I doubt anyone has ever accused MI6 of using the citizens of London as human shields.

What Hamas and Hezbollah are doing however is placing their infrastructure and even weapons platforms directly next to, on top of, underneath and in civilian structures like housing, schools, hospitals, etc., precisely so that there are only bad options for Israel: Either they don’t strike and have to then live with being shot at or otherwise harmed by these structures - or they do attack them as is permitted by the Geneva Convention (any civilian structure used for military purposes uses most of its protection), but get roasted by a part of the Western public for doing so.

Here’s an excellent study on this topic, in case anyone wants to learn more:

https://stratcomcoe.org/publications/hybrid-threats-hamas-use-of-human-shields-in-gaza/87