Well you can cite evidence from the show to back up whatever your preferred interpretation of the character is, because his characterization has never been consistent! Yeah, sure, Pertwee's doctor was extremely overtly scientific, except when he randomly started using magic in "The Ambassadors of Death", which, by the way, was written by the show's first script editor, who you'd think might have some inkling as to the original intent of the character..
Absolutely, the show is grounded in science. Problem is, it's bad science at best, outright pseudo-science at worst. To invert one of Clarke's Laws, any sufficiently bad science is indistinguishable from fantasy. A "counter-earth" on the other side of the sun? Nonsense. The Fourth Doctor's explanation of dimensional transcendence to Leela? Pure gobbledygook. Travelling backwards in time? Not, as far as anybody can figure out, actually possible. What's left? A staggering array of cheap bug-eyed monsters, rock quarries standing in for alien planets, and endless chases through studio corridors to pad out the running time. Oh yes - and also improbable amounts of ingenuity and creativity devoted to the service of a show about an absurdly clever and tirelessly compassionate character. No, I don't see any inconsistency between Moffat's vision of the show and the parts of the show I like best, not at all.
Changing the mythology? The mythology of the show is self-altering. I have a hard time differentiating between people complaining about Moffat ruining the story engine and the Lofficiers' review talking about how "The Deadly Assassin" was the WORST EPISODE EVER and completely destroyed the mythology of the show.
Doctor Who is an inconsistent show, sometimes maddeningly, sometimes gloriously. It has also, since the show's second episode, been about change. I have little patience for so-called "fans" who fail to recognize that basic reality underpinning the show's extremely nebulous story engine.