Rodney got super pissed at John for his flirtation with Chaya because Rodney saw that as John's libido endangering the security of Atlantis, i.e. John failing to do his job. Excellent point.

Before I saw Tracker, I firmly believed that Rodney would get better after The Shrine and then be unbelievably pissed at Keller - not only because her distraction put his life at risk but because the him she was so smitten with wasn't the real him. If it were me, behaviour like that would make me want to smack them, not ask them out.