Yes, he did, but what he knew was going on up there was sex, not love.
An OT observation about the mountain scene with Aguirre:
IMO, this wouldn't be the first time that young males working for Aguirre had sex to relieve tension (re Annie Proulx' quote). What seems to really disturb him on his unexpected visit is the discovery that they've changed roles: Ennis up with the sheep, Jack back at camp. Aguirre might not have given either much thought; but the two together suggest a domestic arrangement that goes a bit beyond sex as a physical release.
When you think about it, that's a foundation of the opposition to same-sex marriage. It isn't so much opposition to same-sex activity as to the suggestion that there's something more than that. It's the people who are often accused of being "heteronormative" that are the real threats to the NOM organizers of the world.