Like, look how much trouble they had with publishing Ulysses, decades later: https://en.wikipedia.org/wiki/Ulysses_(novel)#Publication_hi... . And Ulysses had the benefit of being far less obscene than the diaries, and was Great Literature (TM), rather than, frankly, some pervert's private diaries which had never been intended for publication in the first place. I doubt the diaries could have been safely published in full until after the whole Lady Chatterley's Lover thing, at least not in the UK or US (France was more laid back about this sort of thing).
Wheatley _could_ maybe have been more explicit and said "I've omitted the illegally obscene bits", but honestly given the legal environment of the time this would have been asking for trouble.
I think we'll have to agree to disagree (although it would be very interesting if there was contemporary evidence of his actual thoughts and motivations).