Rashi on Sanhedrin 100a seems to interpret it to mean that he died:
גל של עצמות. שמת, דאדם שמת נעשה גל של עצמות.
A mound of bones. that he died, for a person who died becomes a mound
The Maharal in Chiddushei Aggadoth on Shabbath 34a interprets it to mean sudden death:
ועשה אותו גל עצמות. פירוש [מיתה פתאמית] וזה נקרא גל של עצמות כאלו היה נשרף ונעשה גל עצמות, אבל גבי [לעיל] קאמר נח נפשיה בלבד שלא היה מיתה [פתאומית] כאלו היה נשרף.
And he made him into a mound of bones. The explanation is: [a sudden death] and this is called "a mound of bones" as if he had been burnt and turned into a mound of bones, as opposed to [earlier] where it only said "his soul rested", which was not a [sudden] death as if he had been burnt.
In Chiddushei Aggadoth on Avoda Zara 20b, in discussing the phrase: "אמרו עליו על מלאך המות שכולו מלא עינים" - "It is said of the Agent of Death that he is all full of eyes", the Maharal does indeed relate the idea to what sounds like the concept of ayin hara:
ומפני שהעין פועל לכך אמרו בכל מקום (שבת ל״ד ב׳) נתן עיניו בו ונעשה גל של עצמות וכזה הרבה, מפני כח הפועל אשר יש לעין על ההעדר.
And because the eye is an "Actor", therefore it says in every place: "and he set his eyes on him and he became a mound of bones" and similarly many (other quotes), because of the ability of "Acting" that there is to the eye over "void".**
(See also Ohr Hachaim [Shemoth 11 and 23, and Bamidbar 14].)
It also seems plausible that the punishment is, in a sense, midda k'neged midda (poetic justice) in that he mocked - לגלג the words of the sages and he was thus turned into a mound גל of bones. See also the Maharal in Be'er Hagolah (Be'er 6; p.134 in the old set, p. 317 in Hartman):
וכמה גלים וגלי גלים היו נעשים בעצמות האיש הזה על כל דבר ודבר שאינו מאמין, כאשר יראה האדם בדבריו שכל דבר אשר הוא קצת זר בעיניו הוא אומר שהוא המצאה וכיוצא בו.
And how many mounds and mounds of mounds were made with the bones of this man (Azariah de Rossi?) on each and every thing in which he does not believe, as one sees from his words that everything which is a bit strange in his eyes he says it is a fabrication or similar.
My assumption is that if indeed we interpret the phrase to mean that he caused his actual death by "setting his eyes upon him", it would be related to the capital criminality associated with being a heretic (see, e.g., Rambam Hilchoth Mamrim 3:1).
** (It is self-understood that this attempted literal translation is less than insufficient to understand the Maharal's philosophical terminology, which requires some grounding in the philosophical conceptions of forces, actors, and void.)