When you break Akatosh, you're going from unbroken, to broken. Akatosh has himself figured out, then you're like 'svck on this,' and make him have to relearn himself all over again, and until that time, time is loose and really not time at all. So the Tribunal changed history.
I'm reminded of Krishna for a moment. Krishna was an incarnation of the god Vishnu but was serving as Arjuna's charioteer, apparently human; until the day that he revealed his true nature to Arjuna during a civil war. Maybe Vivec was once a warrior-poet, the advisor and friend of Nerevar until the day that Vivec chose the power that the Heart of Lorkhan could give him. At that point he and the other two Tribunes became gods, and history was changed into a timeline with Vivec having been a god long before his mortal birth. But it's not as if Vivec would have said out loud: "Now I'll change history"; I think he had a more passive role in the timeline's change. Do you see the difference I'm getting at?
It seems to me all this was fate. The Velothi exodus, Azura's curse, the wars, the rise of Nerevar to power, the Tribunal's betrayal, and the changed timeline. It was all fated, maybe to help Lorkhan return. You can't really say "The Tribunal should have remained mortal, they shouldn't have followed their culture's dictates of murder". You wouldn't have a story then, anyway.
Anyway, for what it's worth. Sorry to pontificate, I'm no expert.