It seems to me to be likely that what was really bugging Pauline was not the threat of her relationship with Juliet being thwarted in itself, but her aspirations to another sort of life and to the realisation of her artistic ambitions, at least partly through her relationship with Juliet and Juliet's parents. Given the times, Honora Parker might well have been a very dull, ignorant and hostile working-class NZ housewife. She was probably a lot less sympathetic than Sarah Peirse's portrayal, and may have poured scorn on Pauline's aspirations, probably with more venom or at least irritation than we see in the film. This might be a bit of a class conflict reading: Pauline aspiring to a more "refined" existence, and her mother reacting with scorn and possibly anger at Pauline getting above herself. Thus she is the "obstacle" Pauline describes her as in her diary, not so much to her relationship with Juliet, as to her ambitions and aspirations.
In this reading, one can see the girls' idea of their relationship in the light of a partnership of two geniuses (the diaries etc. support this I think), each supporting and understanding the other in a way no outsider can, and not as a primarily "romantic" partnership. Thus it is essential for Pauline to get away from her own ignorant clod of a mother, and join with Juliet, and Juliet's parents, as the latter, and especially Dr Hulme, are seen as supportive of the finer things of life, including art and scholarship etc., and will not laugh at the girls' ambitions and aspirations. Another layer of prejudice here could be the Hulmes's Englishness, Pauline not wanting to be seen as just a rough colonial, possibly Honora laughing at her pretensions etc.
I must say the evidence strongly suggests that neither girl felt any remorse after the murder, even while realising it was wrong. The evidence seems to suggest that even after being arrested they were "happy" at achieving their goal. None of this is in the movie of course. I can only suppose that they had both somehow in their minds relegated Honora Parker to some sort of non-human status, someone not deserving to live, despite recognising that murdering her was wrong in some sort of technical moral sense.
This reading makes sense, to me, of AP's comments now, and her anger at the film's reading. She says that the real reason has never "come out"; that she didn't expect to get anything out of it (I was very puzzled by this when I first read it); and it wasn't this great "I can't live without you". All this makes more sense if we assume that she thought she was helping Pauline to get rid of an obstacle to her (Pauline's) future plans and ambitions, that she was helping her as a good friend, and also as a fellow genius: her comment at the time that they were apart from the law supports this last bit. And of course she wouldn't get anything out of it, in the same way as Pauline would, as it was Pauline's obstacle to a better life being removed, not an obstacle to their continued relationship.
Obviously I am attempting here to enter into the logic of their world, rightly or wrongly. I do actually agree that in some sense the girls were in love, whatever the physical relationship may have been, and whatever its future may have been, were it allowed to run its course. But if what I am suggesting above is the construction they put on it themselves, then or since, one can understand AP's anger and frustration, then and now, at the way the relationship itself has been foregrounded as a sort of adolescent romance gone wrong.