They already did. A while back they adjusted the engine to reduce the huge power numbers. The engine was originally based upon the steriod era of baseball, when that ended they made an effort to adjust the high end power numbers.
As an aside, how many homers would Bonds or McGwire have hit if they played in Coors Field? What would have happened if their division opponents decided to use AA pitchers in an effort to save money? These questions apply more to Sim Baseball than HBD- but they are relevent when compairing HBD results and MLB results.