Yes, they do take into account the difficulty of the major, and even though grad school grades may tend to be inflated, the adcoms are aware that in general science grades are less inflated than other majors. [Though also with science majors they are often concerned whether you have developed writing and analysis skills, by taking some advanced courses in humanities subjects]. But overall, I think that is a stronger background to have than what you would have had if you'd gone straight from undergrad--- and certainly puts you in a MUCH better position to practice IP, since from what I've read you need at least a master's to be competitive, at least for the prosecution side of things (whereas litigators can get away with a BA/BS and don't even have to take the patent bar).
As for how much they take your science major and extra degree into account, that depends on the school, can't really make a quantitative estimate of the impact.
Also: There was a thread on IP programs in the Rankings folder, which has the USNews rankings of schools with good IP programs. I would definitely say Santa Clara would be a good place for you to look.