The text states that The marionette can be armed with any combination of weapons that the character controlling it knows how to use , and you can explicitly channel ki through them for other uses.

Marionettes with cancer to attack with their own strings sounds like a fun gimmick, but maybe it's too cheesy?

Having a Marionette that uses cancer isn't something that I'd have any problem with personally, after all you have had to invest the points to learn both and need to get your hands on the weapons or the materials to make them.

Though with that said I would rule that you can't do it using their own strings since that is the very thing that you use to control the marionette, though granted if your marionette were to be destroyed during battle I'd have no problem with using the now unoccupied strings as a cancer weapon provided they are of sufficient quality to withstand the rigors of it.