The Geneva conventions are not monolithic documents, and they are not completely uncontroversial. I believe the article 51 you refer to is in a 1978 addon protocol that Israel has not ratified. For reference, there is a different article 51 in the original 1949 conventions, that talks about when an occupying army may conscript civilian labor.

Like any other international treaties, the conventions only apply to countries that have signed on and ratified the treaties. The United States and Israel have not ratified the additional protocol, so from their perspective they are not bound by the text.

The original 1949 conventions do have protections for civilians, but they are weaker protections. Ratiometric evidence of civilian casualties is heartbreaking, but unfortunately simply not relevant to the 1949 conventions. Under those rules, if a facility is used by your enemy to harm you, you can attack that facility. Period.

IDF is always careful to portray how they scrupulously follow the 1949 conventions when they speak to the media. Clear violations that become public are referred to investigation.

As in any war, some elements of IDF are almost certainly violating the conventions. But as a USian I don't think I'll get close to understanding the truth any time soon. I basically don't trust any news source coming out of that region any more.