From what I understand of the design intentions here (and I might be wrong), the spy probes ARE supposed to be the drawback, because it's a horrible risk if there's tons of them around. And indeed, on higher difficulties, this is the case. On Misery, I dont dare try more than 2, and even just that second one is very dangerous. A third is outright impossible.
Changes are probably in store for this mission type overall. I seem to recall Chris mentioning this, though I could be remembering things that didn't happen again. But I'm pretty sure that was the case. But for now, they're gonna be pretty much without threat on the lower difficulties. As for what possible changes might happen, no idea. I'm rather hoping for a complete rework of this mission type. The spy probes themselves just never quite work out very well.
