I'm just catching up on this excellent thread, and others have already made some great points about why Ennis can't just buck up and overcome his childhood scarring, why he might legitimately have hesitated to let Jr. move in, etc.
My feeling is that, although Ennis certainly does have problems connecting with his loved ones, the prospect of Alma Jr. living with Ennis is a terrible idea for all concerned.
At 15, she'd be living in a shabby, isolated house in the middle of nowhere, far from her school and social life, with a single dad who is gone half the time -- as opposed to living in a stable family, with rules and limits and the company of her sister, in a house conveniently located in town. I'm sure that, in a pinch, she could have made do and even been happy in the former situation, but no way is it preferable to the latter.
I hate to keep relying on this explanation -- it's my version of the "cigar is just a cigar" argument for dismissing symbolism -- but I think this scene is there mainly as a narrative device, to set up a parallel with Jack and Ennis' situation. It's like the post-divorce scene: in turning Jack away, Ennis makes what is actually a sound and responsible decision not to ditch his daughters -- but that's not the point of the scene, the point is that he's letting Jack down. In the later scene, we're not meant to concentrate on whether Jr's moving in is really a good idea, but on the fact that Ennis is rejecting her offer to live together, just as he has rejected Jack's. That way the ending, when Ennis finally reverses the pattern, offers a sign of redemption and hope.