My only problem with the rapid fire rules is the fact that every round that hits will strike the targeted location. Which, as the OP points out, can become quite ridiculous if you're aiming for an eye.
Fortunately, I am planning to use a slightly modified version of the variant hit location rules found at
http://rpglair.weebly.com/hit-locations.html, which lend themselves to a solution.
The first round hits based on the MoS. The second round hits based on MoS - RoF. The third round hits based on MoS - (RoFx2). Etc..
So, if your weapon is RoF 2 and you hit with a MoS 5 while aiming at the head, the first round hits face, skull or neck, the second round (treated as MoS 3) is randomised between face, skull and neck, and the third round (treated as MoS 1) hits an entirely random location.
It's not perfect, because in the example above you could feasibly hit face, face, foot, but the chances of doing so are fairly slim and I still think that's a preferable result to eye, eye, eye.