Originally the network didn't mind that House WAS the villain, I guess now that the show is popular that's somehow changed. House is the villain to the characters, and the diseases are the villains to the plots.
As for scientific method, it seems a lot of professionals are losing their grasp on it, switching instead to playing the percentages. Auto repair is a good example of the problem, it's just "spend $400 to fix what likely will be the problem" instead of "we'll track down what the problem through the observation of evidence and application of reason, starting from the most simple and likely explanation and then moving outwards", and why do they do that? Because the demands on their time have become more expensive than what they are fixing.