Most new drugs today win on marketing, rather than efficacy. Once you have a system like watson, it's rather trivial to do the expected value calculation of "This treatment has an X% chance of working, and costs Y. The competing treatment has X'%, and costs Y'."
As long as that data is available to patients (and it should be), I'm with the parent poster, this will make it harder to pad treatments.
The customers for the software are the hospitals that people go to, not the insurance companies or the patients. I guarantee you that the hospitals will prefer whatever option results in the best possible financial outcomes for themselves.
That's actually what they are already doing when pitching new drugs to doctors. Now they only have to convince the system designers and not thousands of practicing doctors.