They're not, they shouldn't, and please, no. Ghostcrawler himself just hit the forums to point out a few good, solid, technical reasons. To sum up his excellent explanation, Blizzard can't just duplicate all the spells and make them work different in PvP and PvE because that multiplies the level of complexity in the programming. The more complexity you add to the system, the more likely you are to see bugs and exploits sneak into the game. Not to mention, on the other side of the fence, the PvP dynamic itself is so complex that you can't just assume "low damage" is a function of the game itself. It can easily be due to the metagame, not to mention each player's performance.
Ghostcrawler's logic seems to be a slam dunk, but I've had the misfortune of playing in a few games that did use different rule sets for PvP and PvE. It's a nightmare. City of Heroes was so clumsy in its divisive handling that I still wake up at night screaming, "That was my power move!"
WoW isn't an either/or game. You don't tend to completely eschew PvE when you're playing PvP, no matter how much we wish you could. Dailies, raids, and other circumstances force you into the world. Even dedicated PvE players jump into the BGs occasionally. Separating the rules between the playing arenas creates yet another barrier to playing the entire World of Warcraft. Not to mention, if those different rules are different enough, it ends up feeling like you're running two different characters. Is that really the game we want?
It's open warfare between Alliance and Horde in Mists of Pandaria, World of Warcraft's next expansion. Jump into five new levels with new talents and class mechanics, try the new monk class, and create a pandaren character to ally with either Horde or Alliance. Look for expansion basics in our Mists FAQ, or dig into our spring press event coverage for more details!