You are right, except that they are also going to be able to determine the transfer functions by stimulating then measuring responses as well as monitor multiple points simultaneously to hopefully uncover algorithms. Of course, this is a long-range project and you are right that there is much more to it than just parts-list and wiring diagram :)
Figuring out the part list and interconnects do not equal understanding how it works. Just like plotting out the circuit diagram of a computer computer does not equal understanding how a CPU works. The brain of Einstein is very similar, if not exactly same, in design to all humans. The reason it worked better must be hidden beyond the mere part lists and wiring diagram. It is a necessary first step though.
One use your allude to, but don't mention directly, is rewiring neurons to control prosthetics. Many neural interfaces are being tried today, but there is too much trial-and-error involved. However, by using the probes to determine exactly which neurons are still functioning normally, it should be possible to implant electrodes that give amputees control over electronic prosthetics that completely restore a patient's lost functionality. Yes, these humans would be "half robot," but much to the patient's benefit.
The researcher do, in fact, plan to stimulate neurons with their probe in order to fully characterize their electronic "transfer function" which will be valuable in understanding how diseases like Parkinson's causes brains to malfunction. Of course, any tool can be misused, but these experiments will be conducted on animals. The only mention made by the researchers regarding use on humans was using the probe during brain surgery to determine just which neurons are diseased, instead of guessing or using trial-and-error like they are often forced to do today.
I interviewed the researcher directly who hopes that the parts list and wiring diagrams they discover will be used by such projects in the future. Their first priority is curing brain diseases by characterizing the signature of abnormal neurons, but they will also characterize normal brain functions, which will be invaluable to projects like DARPA'S SyNAPSE.
I laughed at hearing about your fantasy of enabling your cat to talk, but the more I think about it, the more this seems feasible. By using the robotic probes to determine just which of her neurons are firing when she is hungry, for instance, it should be possible to rig up a vocal response when that feeling is present. Of course, the voice would not really be "hers," but the feeling of hunger would be, and that seems good enough for me (after all a talking robot has to borrow a human voice to speak too). Good idea!
A very interesting topic...I appreciate the dedication of the research team who is going to turn the fiction into reality. I used to think about doing something similar (but might be different) in my childhood. I used to think if it is possible to decode a thought process happening in brain into electrical signals/codes...can this be then applied for "thought reading"...especially for animals? I used to think of applying the technology to my pet cat to enable her talking :)