I agree that several of the problems w/this ep are related to rushing... not even mentioning the atmosphere or gravity questions and the quick wrap-up, for example. It's like they had to cut it down for time.
The question of the TARDIS not liking Clara is pretty obviously the most important thing going forward... I agree that it's not likely to be just a throwaway phrase. And River was never in the TARDIS while she was an active threat to the Doctor, only afterwards [and before, pre-natally]... but it's got to be more than just that she's a threat to him. Bad guys have gotten inside many times.
The TARDIS has frequently allowed multiple versions of the same person from different points in their timelines to be inside together, beyond even just the multi-Doctor occasions, so it's more than the different incarnations of Clara.
I still like my "Eternal Companion" idea.