I'm wondering where the current boundaries for language and topics are in YA fantasy.It's clear your beta reader hasn't read much YA published in the last five years. Not only is the word rape used, so are other words that no one said aloud sixty years ago: lesbian, gay, bisexual, not to mention correct words for body parts rather than silly simpering euphemisms.
In my latest novel, a woman refers to having been raped as a teenager when she refused an offer of marriage by a powerful man. That's all that is said on the subject but it explains something about this woman's situation. One (and only one) of my beta readers suggested the word might be too much for YA. I know I have seen the topic referenced, but can't recall if I have seen the word itself in YA lately. (I know quite a few teens, and none of them would bat an eye at this.)
I'm not sussed about this use of the word but wondered if there is a place to go to get an idea of what the guidelines are these days.
And some of you will remember when the word cancer was never said aloud, let alone on television. John Wayne played the hero in Westerns but he IS a real life hero cause he was one of the first celebrities who talked about cancer in a public forum.
Telling the truth about the world we see is one of the biggest jobs a novelist can take on. Shading that truth for some misbegotten sensibility leads to shame.
Use the right word. If the word is rape, use that.
As for guidelines, this is why you read widely and deeply in your category. You'd know that rape is not a word stricken at the editorial stage by knowing what is published these days. Sadly, all too many YA writers and readers know it is the truth of this world.