Your camera has a burst rate of 5fps, you should be able to get 'em done in a little more than a minute. Let's call it two minutes, that way you get to take a 45-second break in the middle to have a cigarette and a Coke.
In a little more seriousness:
If someone else is managing the line - ideally, someone provided by the company, who knows the employees and can keep them organized - four minutes per person isn't unreasonable. If you have to herd people and manage the line yourself, it's going to take a lot longer.
Tether into Lightroom or Canon's software so they can see the photos as you take them (per request), expect some re-shoots, but don't let any individual hog your setup for more than two or three minutes. Take a ten-minutes break to catch your breath and back up your files after every department (or so).
If it were me, I'd shoot it tethered into Lightroom. That would make it the fastest and simplest, I think. You can set up your white balance in advance, shoot a couple of test shots of yourself or a helper, then set your develop settings (contrast, sharpening, etc) on the test shots. Then, while shooting tethered, Lightroom can automatically apply those develop settings to each file as they come in. Have your company-provided helper move the line, keep track of names, etc. After shooting a few takes of each person, immediately mark your keeper(s) with a flag or star-rating. Then once the last person is done, just filter to those keepers, and export 'em. Shoot, burn, get paid.