The Gemara in Shabbos does not say Apikorus, but rather Gedufi (according to one opinion). If you look at Rashi (DH "Gedufi"), it is unclear whether or not Acher fits that description.

However, your question is addressed in another vein by the Gemara in Chagigah (15b) which asks how Rebbi Meir could have learned Torah from Acher as he did not fit the description of a Malach Hash-m (which a Rebbi should be comparable to as per the teaching of Rebbi Yochanan there). The Gemara in Chagigah explains that Rebbi Meir learned from a Pasuk that one who is already a Gadol b'Torah can learn from such a person Torah, as long as he does not adapt the other person's poisoned mindset.

It should be noted that the RACH in Chagigah (ibid.) says that Rebbi Meir's position is not the Halachah, as the Gemara later says that Eliyahu ha'Navi reported that in Shamayim that the Torah of Rebbi Meir was not said over because he learned it from Acher.

Kol Tuv,

Yaakov