Heya,
I do think you're right that when you look at the situation objectively (without our Brokie-instilled love of both Jack and Ennis, etc.) from Aguirre's point of view neither Jack nor Ennis are doing their job very well during the summer of '63 and they both disobey in their decision to switch roles. So, I don't really fault Aguirre for anger, etc. over that aspect of things.
I still do fault Aguirre over his homophobia (of course) and for his insistence that they do something that's against Forest Service rules to begin with. I don't know all the nuances of that type of work and the culture of sheep herding, or ranching or any of those things. But, as a general rule, if I as an employee, had a boss who asked me to do something that could get us (or me) in trouble, I would be really angry and really question the ethics of the boss.
So, I have a new, unanswerable question (though fun for speculation!) about Aguirre... who do we think he's talking to on the phone at the beginning (the "no, no, no" conversation)?