I want to depower a recursioned factory and can't see a way to do it. I have turn the whole complex off through powerpoles?

Yeah, that's unfortunately the only non-cheating way to do that. If you want to cheat, though, you could try running the command

/c local s = game.player.selected; if s and s.name == "factory-power-pole" then s.destroy() end

while hovering over a factory building's inside power pole to destroy it, so you can then place power manually. I'm reasonably sure this won't break anything else about the mod, but you should back up your save before trying this anyway. Of course you also can't replace a factory's power pole without another command.

it's not perfect but you could turn the power all the way down on the factory power pole too

(all you'd need to do is add a 0W option in the mod)

What about just rotating your power arrow from input to output?

just go inside the building you want turned off and lower the amount of power thats being sent to it to the lowest settings. its not completely "Off" but its close enough.

I frequently use rotating the power from Input to Output to turn off individual factory buildings. It is quick and easy, and works unless it is a power making factory in the first place. It turns off all "inner" factory buildings as well.