I don't remember a rape scene in LOTF - mind you, I haven't touched it since I was 13 and had to do it in school.
I was a precocious reader and worked my way through my mum's bookcase, reading a lot of stuff at about the age of 7 that really wasn't child-friendly. Having said that, I blanked out/skimmed over a lot of stuff that I didn't get, like sex scenes or other nuances.
I read Watership Down at that age, and really enjoyed it. I then got The Plague Dogs out of the library as I assumed it was another animal story - which it was, to be fair, but there was a hell of a lot more adult stuff in it and lots more human-related stuff. I reread it in my twenties and there was so much in it I'd missed.
Actually the thing that freaked me out about Watership Down were the quotes at the start of the chapters - this one in particular I can still recall word for word, it sunk into my brain and creeped me out so much:
When the green field comes off like a lid
Revealing what was much better hid;
Unpleasant
And look, behind you without a sound
The woods have come up and are standing round
In deadly crescent.
The bolt is sliding in its groove,
Outside the window is the black removers' van.
And now with sudden swift emergence
Come the woman in dark glasses and humpbacked surgeons
And the scissors man.
I did not have the capacity to process this as a seven year old and it gave me the screaming abdabs...