^ IIRC, the novelization of ST4 said the probe had previously been able to communicate to the whales from light-years distant that it was enroute and anxious to hear their stories when it arrived, and mankind hadn't reached a technological age where the communications would have caused any problems to man the last time the probe was around. Also, that the ionization effect on the oceans was the probe's attempt to reach wherever the whales had gone into the ocean depths, not realizing that the whales had gone altogether. It didn't really perceive mankind as an intelligence to be communicated with, just the whales, and stopped the ionization effect caused by its "song" only once it heard George or Gracie sing back to it.
I do remember the book saying that the probe asked the whales where they were for however long it had been bombarding Earth's oceans with whalesong, the whales replying that they didn't know, they were there and then and now they were here and now, talking to the probe, the probe asking where the rest of the whales were and the two whales saying that they were all that was left, and the probe departed, wishing them well and anticipating new songs at some future point as it left Earth's orbit, SpaceDock lights up, the rain stops, cue the fanfare.
It wasn't that the probe was trying to wipe out humanity on Earth, but that was just the collateral damage from its whalesong.
If the probe can communicate with the whales over several light years, why couldn't it detect that there were none left on Earth when it entered orbit? If it can talk to them, it should be able to detect them (or lack thereof). Doesn't this thing have sensors?