I guess that depends on what your definition of "less control" is. I would say too short a stem would give you less control, since any minor handlebar movement translates into large angular movement of the wheel, hence a twitchier ride. With a longer stem, you will need to move your arms further in order to get the same angle of rotation of the wheel. This just means you have "finer" control.
Think of it like trying to adjust the hands of a clock. By adjusting near the center of the hands (shorter stem), you're moving the hands faster with less effort but lower accuracy, but by adjusting near the end of the hands, you're able to be more precise, at the cost of more movement/more effort.
That said, I think you pretty much nailed all the points of riding small bikes with long stems -- lower weight, more aero position, etc. At the end of the day, cornering isn't so much turning of the wheels as it is leaning into the turn -- if you're turning your wheels 90 degrees on a descent, you're going to the hospital no matter what size stem you're using
By the way, 52cm for 5'9" doesn't seem too awkward. I think that's the cusp of the suggested height range for most geometries?