James Whorton discusses this historical pejorative usage:

One form of verbal warfare used in retaliation by irregulars was the word “allopathy.” …”Allopathy” and “allopathic” were liberally employed as pejoratives by all irregular physicians of the nineteenth century, and the terms were considered highly offensive by those at whom they were directed. The generally uncomplaining acceptance of [the term] “allopathic medicine” by today’s physicians is an indication of both a lack of awareness of the term’s historical use and the recent thawing of relations between irregulars and allopaths