Whats the real reason Obama wants Arpaio to do things the president's way, for the president's purpose?

It's not just the President. What you should be asking is, why is the President bowing down to the United States Chamber of Commerce, and the others behind them. There are powerful business forces at work in this country that do not want their cheap labor source taken away from them. I believe the investigation actually started last fall, before Obama had even taken office. You could also ask why Congress eliminates any requirement to conform with the Everify program from any bill it gets introduced to. These sources not only don't care about how the employment of illegal aliens depresses American wages, they are actually pleased.