For a "tough guy" Ennis is seen with tears in his eyes a surprisingly large number of times throughout the movie.
Six times, to be exact! (Alley, divorce, lakeside argument, phone booth, Jack's bedroom, final scene.) And one time for Jack (post-divorce). This came up in an interesting thread in a different BetterMost forum, devoted to the subject of crying in the movie.
And Amanda, I completely agree with you that this is among the ways Ennis expresses love.
As for your perspective, Chris, you've touched on some larger disagreements about the movie that would affect interpretations beyond this one scene. Personally, I DO think Ennis sees what he has with Jack as an actual romantic relationship. Not that he'd call it that; he'd call it "this thing" that "grabs hold of us" or some other non-threateningly vague term. But to me there are lots of signs that, as early as their summer on the mountain, and certainly by the time of the reunion, he knows that he cares passionately about Jack (again, he might not use the word "love," but it would amount to that).
So, yeah, I do think Ennis' threat to kill Jack is misdirected rage. I don't for a second believe he'd actually ever hurt Jack. But he's really angry, and not just out of homophobia, I don't think.
But when he says "leave me be," I don't think he really wants Jack to do that. Nor does he really blame Jack for him feeling like nothing and nobody. Again, he's just lashing out because he's upset and scared. He can't stand it any more, but doesn't know how to fix it.
The music and camera angles in that scene provide clues as to how we're supposed to take it, I think. The music is absent while Jack is talking, and the camera is trained matter-of-factly on him -- he's making some good points, and we don't know how Ennis is reacting, maybe he's still angry or whatever. Then Jack finishes speaking, and finally the camera turns back to Ennis and we see that his demeanor has changed, he is crying and REALLY upset and at that moment the sad touching music strikes up full force, as if indicating that, yeah, Jack is frustrated and pissed off, but look how heartbroken Ennis is. As I understand it, we're being shown that, as hard as this situation is on Jack, it's equally hard on Ennis.