I have seen this question many times ( with different devices) . I'm still quizzical as to why anyone would want to use the HT side of a coil. You start talking about direct coupling of a ignition coil, your asking for trouble. Your observed noise picture is deceptive because the discharge generates lots of harmonics and digital electronics dislike wildly varying signals at different freqs. Kind of an AF-RF white noise . Just take the input side of the coil/mag and use it to spec . 1 pull up resistor and your set.
Edit to add: If You insist on the HT path many amplifier repair parts suppliers make an opto isolator for old Fender amps in the tremolo circuit. Input side is a neon bulb, output side is a fast photo resistor. Or make one your self, a neon and a PR joined with black shrink wrap spaghetti