Percentile alpha control in the Compositor? Is there a way to adjust the transparency of an image in the compositor with a percentage of the alpha of the original image? 

(So images that pixels that are completely transparent stay that way, and pixels that are partially transparent stay the same relative to the rest of the image)
Yes by using math.

The alpha channel is a value from 0.0=transparent to 1.0=solid. A math node can be used to multiply alpha values by the value you want to use. Which you then feed into the alpha over Fac to combine the images. You can also use a CombineRGBA to join together depending on your needs.

While multiplying a zero value by 0.5 leaves it zero you can use math node to get values greater than 0.99 if you wish to only effect a non-transparent area.

You can also use less than to pass through unaltered values and add them together before the alpha over.