Well having a more powerful +5vdc regulator on-board regulator is not unsafe on it's own, but I just don't think there is any real useful advantage for upgrading the on-board regulator. A more powerful regulator is going to require a larger heat sink to reach it's max rated current anyway, so on board room will be a factor. Also there is a one amp polarity protection diode wired between the board's external power connector and the on-board regulator so that has to be upgraded also if you wish to keep that protection.
It's better if you explain what problem you are trying to solve specifly. What external devices or components are you wiring to the Arduino?
Also you realize that any increase in +5vdc current you gain with modifications won't be avalible when you are powering the board with USB connection only?
Lefty