A response to the above referenced article was written by Yair Hoffman and is available online.
I skimmed through it and noticed two things.
He says there is no geographic connection timeline connection between the pagan custom and shlissel challah.
Also, the lack of early references to this minhag is explained simply that Chasidus only exists since the Baal Shem, so there wouldnt be any previous mention. I would guess that with many chassidic minhagim you wouldnt be able to find early references to them. This does not mean they are wrong.
He also has an early source—-
“The earliest reference is in the works of Rabbi Pinchas Shapiro of Koritz (born 1726), a descendent of the Megaleh Amukos and a student of the Baal Shem Tov. In his work called Imrei Pinchas (#298) he explains that the reason to bake Schlissel Challah on the Shabbos following Pesach is that during Pesach, the gates to Heaven were opened and remain open until Pesach Sheni. The key alludes to the fact that these gates are now open and that we should focus our prayers ever more on that account.”