仇 is not an alternative form of 敵 (there's a word 仇敵【きゅうてき】). And aside from it, not being 常用漢字 doesn't mean immediately the kanji is rarely used. Kanji frequency distribution usually shows a long tail, and the rank varies depending on the source collection. According to @scriptin's investigation, 仇 is at #1951 among novels in 青空文庫, as well as #2280 in Wikipedia JP, so you can see it's a pretty close loser to 常用漢字 (now has 2,136 kanji).
In my personal experience, 仇 for the word かたき ("foe; rival; who should be avenged on") is a fairly well understood, or perhaps more preferred way of writing, partly because 敵 stands for another well known reading: てき ("enemy; opponent").