OK, correct me if I’m wrong, but he lives in (or at least spends a ton of time at) a batting centre, right? And it definitely seems like (though I could be completely wrong) all his ideas of how school works come from manga or something. I wouldn’t be surprised if he spent the rest of his time in a manga café, or if he’s more or less a stereotypical otaku/hikikomori on the inside. (Quick thought: It honestly looks like a pretty great story, to the point that I might add it to my watch list and I’m wondering why I didn’t hear of it earlier, so I’d like to keep discussions of spoilers to a minimum. In other words, no real need to tell me if I’m right in detail.)
The rest of what I’m going to post will contain a brief analysis using stuff that happened later in Episode 1, so I’ll cover the spoilers up (and endeavour to make sentences that convey the gist even with the spoilers hidden):
OK, honestly, I think it really did mean ‘rape’, or at least ‘violate’. I suspect that it’s actually meant to be shocking, but also to be written off almost completely by the audience because of his ridiculous actions in the next few seconds. (I’m assuming that the anime is a faithful adaptation of what happens next in the source material, of course.) As for why it can be written off, besides how ludicrous he looked crawling around under a box, you’ll need to examine his character and what happens later for an explanation. Most importantly (and this is where my ‘manga café otaku’ hypothesis comes from), notice how he reacts when he sees that gym class will be co-ed and Shizuku tells him she’s going for class: he undoes his buttons and belt buckle, looking embarrassed, and then abruptly strips them off, as though he’s saying, ‘Take me, Shizuku!’ (He gave her a 告白, remember?) That probably indicates that he has some weird concept of how human interactions, especially between men and women, should go, especially in the context of school, perhaps based on a rom-com/ecchi/ero manga. In other words, his behaviour and choice of words are likely meant to show exactly how ridiculously unsocialised he is, and how mistaken he is about how to interact normally, to the point that he doesn’t know how shocking what he just said is. One other bit of evidence pointing towards this: how he asks about how Shizuku’s day at school went. He clearly thought it was normal to get someone to talk about what had happened by accusing her of pretending nothing had happened, and very violently at that. It’s just another example of Haru choosing excessively violent words that have no need to be used in a particular situation.
If you’re trying to figure out how the characters themselves could have written it off, I think it’s really because of Shizuku’s character. She’s portrayed as very unemotional.
I’ll go search around a little more, but that doesn’t match the meaning associated with the kanji chosen in the manga, and as far as I know, all forms of おかす involve some sort of violation or infringement, even if it’s not sexual. None of the Japanese definitions I have really match ‘hurt’. The closest one is this:
② 女性に暴行を加える。姦淫する。
暴行 can refer to violent behaviour in general. It is ever so slightly ambiguous. However, 女性 is specified as the recipient of the action, and 姦淫する (=‘(of a man and woman) to have improper carnal relations’) is listed as a synonym. There’s at the very least a slight suggestion of sexual violence, even if, as I said in my analysis above, it’s not meant to be taken seriously, even if it’s shocking.
(The linguistic and legal spheres aside though, this is quite a horrible thing to be discussing. 
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