In my opinion, Aguirre is less homophobic than you might think. Not only does he not fire them, which would have been inconvenient, but he doesn't even mention the rose-stemming that whole summer! He says nothing about it when he tells Jack about Uncle Harold (when he could have said something about having just seen them fooling around), and he says nothing about it when they're doing the final sheep count (when he also could said something like, "Count ain't what I'd hoped for, neither -- probably 'cause you two left the dogs to babysit the sheep while you stemmed the rose!").
And when he finally does mention it, when Jack goes looking for work the next summer, and he says, "Ain't got no work for YOU," we assume he means because Jack is gay. He might very well have not hired Jack anyway, since we was displeased with the sheep count the two times he did hire Jack. And he mentions the rose-stemming only after Jack asks about Ennis. In a way, it's almost like an afterthought.
And maybe Aguirre really wasn't as scandalized by it as we might suppose. After all, wasn't it Annie Proulx who said something about herders deliberately being sent up in pairs so they could, um, keep each other company? Or maybe Aguirre views Jack and Ennis as behaving like men in prison -- supposedly straight men having sex together only because there are no women available. After all, when Aguirre does mention it, he doesn't say, "I know you're queer." He complains about their work habits, not their sexual orientation.
Some have said they think Aguirre himself is gay. I don't think we see any clear evidence of that.
But I do think he's like Old Man Twist -- less homophobic than we might expect, given their time and place. I was struck by this oddity the second or third time I saw the movie (along with Alma's keeping secret what she saw). And I assumed it was because the filmmakers wanted to keep more focus on Ennis' inner conflicts and less on homophobic treatment they experienced from others.
