If there was malware in Matrix I’m sure the many people who have looked at the code would have found it by now and we’d hear all about it. It’s also worth noting that most Matrix servers you can choose are not in Israel.
And Signal is not a good alternative, as just like Microsoft here, they can ban you if they don’t like where you’re sending messages. Not that they will, but they have that power.
Free/open source software is an international development effort. Whether some developers are Israeli is irrelevant because the code is public and has developers worldwide.
And they are famous for spyware, yes, but that’s from specific state-sanctioned companies. Like NSO group.