When your script calls for ignoring a request to stop... don't be surprised when your request to stop is ignored.
Safe words, indeed.
Something to inform the other(s) that you are stepping outside the role, that this is for real, not roleplay.
While he was a reluctant participant, this wasn't as great a concern, as the likelihood of his pushing a scene was low.
Now that he's starting to enjoy watching her reactions, the likelihood of his unknowingly continuing after she really has decided she wants to stop increases significantly if there is no pre agreed upon method of breaking the scene to discuss what's going on. Really, that's what happened just now.
This really should be a wakeup call for them.
Unfortunately, it looks like she hadn't done any research on how this type of thing should be done, and as it wasn't anything he'd been interested in previously, he hadn't a clue.
She's working from the various manga she's read, and the thing with those is that what's being portrayed may not match best practises; that will depend upon whom the manga was actually targeted at; if it's targeted at those who get off on non-consent, no way are they going to show proper practice for those roleplaying at it.
That does not excuse him from not doing research now; after all, they just experienced his pushing things beyond what she wanted to do because her resisting was scripted into the play and thus he didn't realize that she really did mean it, and they discussed that afterwards so he has to be aware that it's a very real problem.
A number of previous commenters used the abbreviation NTR, which I've determined is short for netorare.
It's unfortunate that the English Wikipedia redirects that term to infidelity, as from the use here I'm thinking that what's being referred to is shifting from consensual to non-consensual without the one party realizing that the other has ceased to consent, which is very different from infidelity.