That would be a task of compositing using something like Nuke or After-Effects. Here's how I'd tackle something like this:
Grab a frame of the person looking directly in the camera
Track the positions of the eyes ("track_left" and "track_right" as seperates)
Mask out the eyes from the still-frame and separate them into eye_left and ...
As mentioned in the comments, I realized that Premiere Pro was the wrong tool for the job. Thanks to Florian I got started with ffmpeg.
For the sake of any future users who might want something like this, I thought I'd share my solution.
The following Command helps me convert my wmv source file to mp4 with a png watermark in the bottom right corner and the ...