I was just watching the movie again. Well, it seemed to me that at their reunion, when Ennis introduces Alma to Jack, and tells her they're going to go to a bar, and may stay all night drinking and talking, Ennis feels bad for having to lie to Alma. I think that in his own way, he loved her. He wasn't in love with her, but he did care about her. After all Alma was the mother of his kids. I don't know, but there's something in Ennis looks when he's putting his hat on to go with Jack, that made me think that deep in his heart he wished he didn't have to lie to Alma.
Poor Ennis. He was a total mess. He was happy and excited to see Jack after four years, and at the same time felt truly bad for hurting Alma. I'm not saying that he suspected Alma knew. I don't think he did, but he does notice that Alma feels bad and left out, I think. At the same time he couldn't help the situation, neither knew how to, although he sure wished he did. So sad