I have argued about this before, notably with Jeff, who made some persuasive points. My own position on the gauge -- pure jealousy on one end and pure homophobia on the other -- has always hovered closer to the jealousy end. But I'll have to say, Clarissa, that your vivid image of an internal lynch mob nudged it a notch or two toward the homophobia end.
Still, I think Ennis' primary emotions here are anger and fear, in reaction to Jack's grim manner and ominous past-tense "I did, ONCE," and his suspicion that Jack already has been unfaithful and may be slipping away altogether. And as we all know, when Ennis feels overwhelmed by scary emotions his impulse is to try to control them with violence. (Speaking of good images, I love Anthony Lane's phrase that Ennis acts as if "the only option for the unrequited is to waylay one's own heart and beat it senseless.")
When Ennis says "boys like you," it suggests to me that he already has at least partly acknowledged what kind of boy Jack is, if not by extension himself. He doesn't say he'd kill Jack because he IS a boy like that, he says he would kill Jack if he personally were to be made aware of his specific boyish activities. As to what Ennis thinks HE is, you'd think he'd have noticed at some point that he finds men more attractive than women, and that if he was able to suppress that feeling when he was 19, over the next 20 years that realization would at least give him pause.