As for the TARDIS not liking Clara, I think that people are forgetting that the ship did more than lock the doors. The ship made a noise and the lights flickered dangerously, like someone expressing disapproval and/or anger.
Science has always been dodgy in this franchise. I remember reading commentaries on this series, published by Mad Norwegian Press, in which the commentators discussed the science and demonstrated how flawed it was.
I think the TARDIS, as an individual, selects which languages are translatable, based on her own subjective evaluation. She does seem to have given the Doctor greater latitude in the navigation of the ship; it was a running theme in the franchise that the Doctor would select one place and land at another.