Is there a way to fixate the diopter adjust knob on Canon DSLR?

Is there a way to permanently disable/fixate the diopter knob on pre-set value?

I doubt it. The knob seems to be mechanical, and there’s nothing like a “locked” setting. I don’t think you’d want to remove it entirely because you’d have no way to fix it if it ever went out of adjustment, or if your eyes change. Perhaps the best solution is to arrange your camera bag so that the camera isn’t jammed in there too tightly, or change the orientation of the camera in the bag. I’ve had the same problem you describe, but only when the back of the camera rubs against the wall of the bag. It’s never an issue in a messenger-style bag where the camera goes in with the back facing up.

Or it has to be a habit of checking the knob position every time I start shooting?

It’s a very quick thing to check — when you look through the viewfinder, just try to notice if the displayed data (shutter speed, aperture, etc) is sharp or not.