> "Which, to my knowledge, are only currently generated using a nuclear weapon. You might be able to create one using solid state gear with enough time, R&D, and power."

Some use a nuclear source, but not all... https://en.wikipedia.org/wiki/Directed-energy_weapon

> "Machine intelligence frowns upon your silly attempts at jamming its uplinks. Predator drones and other autonomous, existing military kit already use high frequency satellite communications techniques that are essentially jam proof."

Your idea of jamming is too narrow. Think about it like this, even if it's mostly automated, these machines still get sent signals to inform them of changes to their mission. That signal can be blocked and/or modified. Even satellite links can be altered, either you hack the satellite system or you intercept the signal at a higher altitude than the receiver is operating in.