if you're going to use a foot controller, then I imagine you are not interested in a computer controlled (CNC) XYZ table, is that correct?
unlike a drill press, the laser won't stop drilling once it penetrates the substrate. Further, a 60W CO2 laser will slice through some materials so quickly, you'll want fractional second pulse widths... to several decimal places. Meaning, no matter how fast your foot is, it will hold the foot switch down too long.
If you hope to have your hands in there, and move the substrate around while its lasing, then you have a good shot at winning the Darwin award. Bad, bad, idea. No insurance company will insure you, and OSHA will definitely prosecute if they find this in a commercial shop with employees.
One more thing, you can't see where a CO2 laser is aiming, because its invisible, so you'll want to use optics and combine the CO2 beam with something in the visible range, such as red or green.
With all this said, believe it or not, there are multiple sources in China that sell the tubes, power supplies and most of what you need to set this up. Unlike most other gas laser systems, the gas tube in these systems are the least costing component (nearly, anyway)
If I were setting up my first CO2 laser system, I could see myself considering a drill press concept like you're discussing. But once you see what it can do, you'll realize you're playing with plutonium in a setup like this.
Consider locating a shop using a CO2 laser and go see what it can do.
Yes, we mess around with lasers, here. But for the most part, we work in the visible spectrum, so we can see the damage to our eyes coming. The things a CO2 laser can do to the human body, is like comparing a tricycle to a freight train.