I think Ruby shouldn't be the submissive one here. She's nearly as frightened and confused as Tom is, seeing herself murder her only friend in this place.
Instead of being submissive and apologising, she should scream at him, tell him that she doesn't remember anything more than he does, ask him if he really believes that recording, showing her do stuff she wouldn't even think about, didn't hurt her as much as it hurt him - and then break down in tears, throw the scalpel at him (in a harmless and nonhostile way), move aside, and demand that he fucks off and leaves her alone.
Besides, bad guys in these situations always laugh and go "that's ridiculous" or "you really don't believe that, don't you?". If Ruby doesn't pull that off, Tom will know she's logically a good guy.
Also I very much doubt that Tom's willing to just club her to death.