It seems like every time I ask a question in a device specific community people are more interested in defending the device than helping to solve the problem.
That's one way of looking at it. The other is that they disagree with your unshakeable confidence:
At this point it's obvious to me that the ESP (or likely something I did with it) caused this to happen.
You're running complicated software on your MacBook (linux) that's riddled with bugs. That's not a criticism; it's a statement of fact for all of the popular OS's.
Sure, there might have been some interaction with USB and booting or whatever and your disk got corrupted. Welcome to complex software. Things go wrong.
Your unshakable confidence that an ESP32 device somehow has malware and is infecting/corrupting your Mac and Pi is not warranted.
Did you know that the ESP32 doesn't have a USB port? Did you know that pretty much every ESP32 board with USB port has a USB to serial chip (CP2x0x or CH340 or similar family). The USB serial chip has transmit and receive serial connections to the ESP32 and two other lines that can reset the chip and control the GPIO0 input for putting the chip into flash mode at reset.
Even if your ESP32 has some crazy virus (it doesn't), it doesn't have access to the USB port on your ESP32 board.
And, the article you posted about the ESP32 and malware is blown completely out of proportion (hint, websites do that to sell clicks to people like you). The article is talking about an issue were some bits of configuration memory can be irreversibly changed. The ESP does not execute programs from that memory.
There is a 0.0% chance your ESP32 is infected with malware.
You now think I'm just one of those people 'defending' the ESP and not taking you seriously.
Sorry. It's just the way it is. Your disk got corrupted. It happens. Fix it and move on. It's not due to malware on your ESP32