This is actually a very accurate summary of one of the key aspects of Joyce's style as an author. He is a writer who hints at things, rather than spell out what precisely happens. In particular, the relationship between the boy and Father Flynn is something that is cast doubt upon though no outright accusations are made. Rather, Joyce leaves things unsaid and unthought and merely points out details and suggestions leaving his readers to draw their own conclusions. Consider what the boy thinks at the beginning of the story as he passes Father Flynn's window:
Every night as I gazed up at the window I said softly to myself the word paralysis. It had always sounded strangely in my ears, like the word gnomon in the Euclid and the word simony in the Catechism.
The word "gnomon" actually indicates a hand on an instrument that is used to indicate something. This is precisely Joyce's style: he indicates, but no more. He does present us with hard and fast conclusions, and through ellipsis only allows such disturbing thoughts to remain as mere, intangible suspicions. Note how the story ends with Eliza relating the laughing incident the analysis refers to:
Wide-awake and laughing-like to himself... So then, of course, when they say what, that made them think that there was something gone wrong with him...
The ellision indicated by the three dots signals words and thoughts that remain unuttered, and merely hint at something more disturbing and sinister. Therefore, in conclusion, the analysis quoted in this question is accurate and highlights a key element of Joyce's style in this short story.