I don't know how to measure foot supination nor have I successfully measured similar rotatory body motions.
I have a similar problem - to measure wrist pronation during a tennis serve. To see pronation (between the elbow and wrist) and to separate it from upper arm rotation (internal shoulder rotation) the angular difference between the elbow and wrist must be measured (in this case from a single viewpoint camera). I have videos that show internal shoulder rotation very well but it is difficult to get the wrist position from the videos without markers because of the quality of the videos. I cannot place markers.
If I could place markers and duplicate the set up after the original videos were taken - and maybe you can? - I might use markers as placed in this report on baseball pitchers.
Look at the markers used to indicate shoulder angular positions for baseball pitchers, photos page 51.
http://www.jssm.org/vol7/n1/7/v7n1-7pdf.pdf
Place the swimmer and camera in the pool as originally taken and place very clear markers on the swimmer's foot, leg, etc.. Of course you can do most work to develop and try out the technique without the pool. Calibrate marker position vs foot supination in the video. Maybe you can get a reasonable estimate using the markers and then use that as a guide/template to estimate the foot supination in your data videos. Could Kinovea lines be used to construct a calibrated scale for supination given the set up is nearly the same.
[Term Usage Pronation. I recently realized that my understanding of anatomical pronation was uncertain for the hand. I believe, but am not certain, that pronation for the hand is defined as the angular position in degrees from an anatomically neutral position. Bend elbow, thumb straight up/vertical. Rotation of thumb in medial direction gives degree of pronation but in lateral direction degree of supination. In other words, I'm still unclear if by definition pronation is only an angular position (degrees) and if used for a direction of motion (counter clockwise) the term is not being correctly used. Uncertain of usage..?.. The sloppy usages of the term "pronation" in tennis is ridiculous.]