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.

You could remove it altogether.

1. Set the diopter wheel at the adjustment you desire.
2. While holding the adjustment wheel to prevent moving it use a (correct size & type) screwdriver to remove the screw in the center of the wheel.
3. Lift the wheel straight out of the housing.
4. Replace the screw to close up the opening.

If you don't want to do anything that drastic and you don't currently have an eyecup attached to the viewfinder get one and place it on the camera. It will partially protect the diopter adjustment wheel from inadvertent movements. Check your User's manual to see which size your particular camera uses. Most Canon EOS DSLRs use either the Eb, Ef, or Eg size and are relatively cheap. You can get third party substitutes at very low cost. Some of the knock-offs have been reported to be larger than the OEM part and completely block the diopter adjustment wheel.

I just started having this problem when putting my camera in and out of a Aquatech rain covering. I have a Canon R-5, so they do not make an eye-piece for it. I had to take the stretchy hole where the eyepiece goes and stretch it around the existing eye-piece. When doing that, the diopter moves. I decided to try the tape method. I used a duct tape that is not extremely sticky, and cut it to fit. Another idea would be to put a tiny dot of colored nail polish on the correct setting, so it would be easy to line up if it moves.