Elisha ben Avuyah's (Acher's) fundamental flaw was his priorities. He thought that the Revealed Torah took precedence over the Hidden Torah. Since the Revealed Torah is all about judgement, Kosher, not-kosher, pure, impure, permitted, forebidden, so HaShem is primarily a judgemental God. Also, this is the explanation of Elisha ben Avuyah's encounter with the angel M"T (מ"ט) -- M"T is the source of the mishna, the Revealed Torah, and Elisha ben Avuyah saw him and thought that he was a separate entity from HaShem.
In reality, our life originates in the Hidden Torah, where HaShem is represented as עתיק ancient, a wise merciful God. The Notzer Hesed goes on to explain that study of the Hidden Torah (Zohar and the Arizal especially) is vital for everyone at every level. It purifies one's soul and fills them with Holy awe. As it says in Pirkei Avot: Anyone whose Fear [of sin] comes before their Wisdom, their Wisdom will be lasting; Anyone whose Wisdom comes before their Fear, their Wisdom will not last. So, Elisha ben Avuyah, who put the Revealed Torah, what is understandable and knowable, before the Hidden Torah, which is incomprehensible and is the source of our heavenly awe, his wisdom failed him. And, since he put his emphasis in the Revealed Torah, he thought HaShem to be unforgiving and judgemental.
Instead, even from a young age, the Notzer Hesed says, we should be involved in the Hidden Torah, the root of the world's life force--not to try and grasp and perceive and understand HaShem, but rather to connect to the sweetness of HaShem's ways. This will give us the necesary awe and yirah so that our Wisdom, our studies in the Revealed Torah, that which is within our grasp, will be a lasting accomplishment.
Rebbe Meir said don't look at the vessel, rather what is within it, the Notzer Hesed explains this as well to mean that Elisha ben Avuyah shouldn't look at the angel M"T but rather at the power within him -- which originates (obviously) with HaShem. (Who is all merciful and accepts all Teshuvah)
In short I think it means: anyone who says I won't study the Hidden Torah now, I'll first master the Revealed Torah and then move on to the Hidden Torah, is following (chas v'shalom) in Acher's mistaken de'ah.