The Ovdei Avodah Zarah forced something into our holy Torah
Forced? I hardly think so.
Yes, it became convenient as a reference point for disputations, but I don’t think any non-Jewish authorities ever issued a decree saying “When you print your holy books, you must use our chapter/verse numbering system…”
In any event, if you truly feel that this is so abonimable, you’re free to print a Tanach without perek/pasuk references. I don’t see any of the Gedolim calling for the abolition of these references now that we have the ability to print sefarim with impunity in any manner we like.
The Wolf