Throw minor league stats out the door, they don't matter.
Miles may not be slow, but Harris' speed might make or break some games. Miles speed won't.
Harris can play 2 spots, like you said, which is quite valuable. ...Especially with three middle infielders that are good enough to start on a quality big league team.
Switch hitters are over rated, IMO. ...That is of course, unless you are Carlos Beltran.
Harris is actually a career .237 hitter at the big league level where as Miles is .325. However, Harris has quite a few more at bats, and hits in a park that doesn't give you an extra 7% on the ball.
I'm not sure .368 over .338 is a slight edge. That seems like a lot in terms of on base percentage.
Harris has gold glove potential. Notice I said potential. He may never reach that potential, but he is still pretty good with the glove at 2B.
And those are just my two cents. Not an argument, just food for thought.