I know he brought him the down because a big storm was coming, and the main reason he didn't hire Jack again was because Jack neglected his work and therefore wouldn't do a good job like Aguirre wanted. However, there was some element of homophobia. As for why he didn't tell anyone, maybe he did tell some of his buddies about, and other people he knew, or casually brought it up in a conversation to make fun of Jack and Ennis like saying "you know last summer I hired these two guys to work for me and turned out they were a couple of queers." I can definitely imagine that.
But he lived in Signal, so no one there would have known Jack and Ennis, because right after they parted ways Ennis left Signal to go wherever Alma's family lived and Jack went up north to Lightning Flat to his parents' house. Then later, Ennis moved to Riverton and Jack to Texas, so the rumors about Ennis and Jack would have stayed in Signal, no one outside of there would have known. I still wonder why though didn't Aguirre just fire them from the moment he found out...obviously he was angry that they weren't doing their work. So why keep them on for another month? The only answer for that is that it was just to late to hire anyone else, and he had to keep them till the end of term.
Lucky for him the storm came through, and he had a good excuse then to get rid of them earlier. But I do agree that the main reason that kept Jack and Ennis apart was Ennis himself. Yes, I sympathize with him because I know what kind of society he lived in, and I can completely understand his fears. However, him caring too much about what other people think, and him being in denial make me very frustrated with him, the way poor Jack must have felt, a mixture of love and frustration. Ennis himself was his own worst enemy sometimes.