For what its worth, in the past (d20 campaign) permanency was tied to more than a single bad die roll on a savings throw. The loss of items at the first BI only came after a table outright failed a mission and did not get off the board - ergo being captured. That is something that can be attributed to player action rather than a bad die roll.
Likewise, every permanent detrimental effect I can think of from the d20 campaign was tied to character action, inaction, decision, or the overall campaign plot. These sorts of things are thematic and make Arcanis what it is.
I don't actually remember ever having seen any untreatable permanent detrimental effect in the first campaign that was attributed to a single poor die roll, but it was ten+ years ago so I could be mistaken.
My overall take is that had the effect been from an optional encounter (like breaking open a tomb), a player decision (drinking from a cursed chalice for example), or otherwise something that was directly the result of a player action, then I would whole-heartedly support the idea of having that PC live with the permanent consequences. However, that was not the case here to my knowledge - this is an encounter that the module expects every table to complete, and the only thing the players did was walk into the room where the monster appeared. There is no way to my knowledge to avoid having to make the save (barring some specialized spells that most tables don't have), and anyone whom rolls badly on that save is subject to the permanent effect. The old Arcanis adage was always "Stupidity leads to character creation, not bad luck"
This situation was not one borne of stupidity, but rather can most accurately be described as bad luck.
Thanks for reading, I hope that my take on it is helpful in some way