I wholely agree that there must not be any ranking of religions, either through tech trees or relatively advantageous traits, for that would be disrespectful and insulting in the extreme. Even if history has "shown" that certain religions came after others, the underlying premise of Civ is a historical "what-if" game, not a simulation of the history of the real world.
The problem with the having real world religions and assigning traits to them is that it perpetuates stereotypes (based, especially, upon American views of the world) and Civ currently has a market in a large number of countries beyond the U.S. Even if that essential fact was not true, it would subtly embody the worst elements of American mass culture--arrogance and insensitivity, especially in a pluralistic society. By this, I am not denouncing American culture (being an American myself!) but am merely advising against perpetuating elements that we should be trying to mitigate and eliminate.
Therefore, slightly off-topic, I also do not like the idea of pre-set civ traits. I do not think players should create their own civs every game, however, and would prefer some kind of "organic evolution" of traits.
Anyway, with my customizing traits/practices and custom naming (possibly saving certain trait combinations as templates to be re-used), players can still experience the historical immersiveness that connecting to reality would allow, except that players would create the connections themselves and therefore be more comfortable with it. And for those who would rather not connect with reality, they could as well make the Religion of Worshiping the Green Dot...