You're right about Aguirre not seeming too hostile in his tone, but the look on his face seems to suggest that he's less than enamoured by what he's seen. He doesn't say anything then, sure, but when Jack goes looking for work again the following year he makes the comment about "stemming the rose" and tells Jack to "get the hell out of my trailer" - which, to me at least, suggests someone who would not be willing to employ someone that he knew was gay (or at least knew was having homosexual sex) His tone in that scene is definitely at least halfway to hostile too.
You are paying these two people to do a job. When you go up there they aren't working. You can assume this isn't the first time they "took a break" from working in the middle of the day when they should have been working. Then, they come down off of the mountain and you discover the number of sheep isn't what you had been hoping for either. The loss of one sheep is a lot of money.
Would you hire them again?
Even when Aguirre tells Jack he saw them, he gets a slight grin on his face before the says, "You boys sure found a way to pass the time up there." Then he says, you weren't being paid to let the dogs babysit the sheep while you two stemmed the rose. Again a comment on their work habits. He could just as easily said, you weren't being paid to let the dogs babysit the sheep while you two played poker.
Look at the scene; Aguirre sees them, looks at his watch, waits a respectable amount of time to let the boys finish, get dressed and go back to work, comes over to Jack, tells him what Jack's mother wanted him to tell Jack and leaves. He didn't even want to embarrass Jack by telling him they needed to do more work and less fooling around.
No, I just do not see Aguirre as this evil homophobic villain.