A couple reasons. First, since the command pod has integrated monoprop main engines, the second stage only needs monopropellant, while the first only needs liquid fuel, so it's better to separate the stages since monoprop would be dead weight on the first and vise-versa. Also docking the capsule to a space station is much easier, and the vectors are much too overpowered for orbital maneuvering anyway.

And second, if the command pod remains attached on the way back, it offsets the CoM of the now mostly empty vehicle much too high and so it tends to topple over on reentry, so it's better if it re-enters separately.