Safe is a function of the head you use, the correct counterweighting, and the tripod/stand/dolly.
This is one of those instances where a direct connection between the head and the camera body may be a better idea than a quick release -- unless the QR plate is completely captive at the head (either fully enclosed or mechanically registered with a pin) and uses something other than a toggle to open/close the clamp. You'll also want to ensure that the camera can't torque -- that whatever it attaches to either has sufficient contact area with the body or tripod ring, or has some mechanical means of preventing the camera from twisting about. You'll also want to ensure that the head can positively hold its angle with the camera attached (most heads have no trouble with the camera set level, but are less secure at a severe angle).
You'll probably want to use a short, strong safety tether from the jib to one of the camera's strap attachment points as well, just to reduce your hart rate and perspiration levels.
Counterweighting is pretty easy to get right -- you'll want to have the system close enough to perfectly balanced that there is no significant effort involved in raising or lowering the camera, but just slightly overbalanced towards the counterweight so that the camera goes up rather than down when friction is released and you let go of the rig. That's going to involve something more subtle than just the barbell weights the jib uses. You can use the weights to get you close to neutral, but you'll probably need a small sandbag or a water bottle to make the fine adjustments. (You can get clamp- or loop-equipped caps to fit standard water/pop bottles at camping supply stores.)
The tripod will need to be on good casters if you're not using a proper dolly, and you'll need to keep the center of gravity of the whole rig as low as possible. If there's a platform or spider that's designed to be weighted, you're in good shape; otherwise you'll have to find a way to attach some weight as close to the floor as you can get it. (The Manfrotto counterweight/clamp unit used on the three piece boom is a good example of something you can use on just about any tripod.) This isn't a fix for a rickety set-up -- the tripod or whatever should not feel unstable when the rig is assembled, even without the weight -- it's to make it less succeptible to clumsiness and accidents.
As for operation, well, the jib uses a parallelogram, so once you set the camera angle, you're good to go -- it will point in the same direction no matter the elevation you're using. Setting the camera for a direct overhead at a comfortable working level means that it will still be set for a direct overhead when the tripod is cranked up and the jib is raised or lowered.
That leaves framing; and you can use the camera tethered for that. (In the old days, it meant using a pencil video camera looking through the camera's viewfinder, a broadcast-quality monitor and a remote control rig to operate focus and zoom. One adjusted the lighting to change exposure. That's still a viable solution if nothing else works.) I'm not familiar with the Canon way of doing things, but you should be able to use live view to frame and focus on a laptop screen. You will still need to use some sort of remote electromechanical linkage to adjust the focal length of a zoom lens (unless you use a bridge camera -- which seems unlikely given the rest of the setup) or haul the camera down and change the zoom manually as required.