As I said they weren't really 'untempered' as more 'tempered again' - the comments of the npcs in the cell in Zan'rak definitely hinted at it. And in any event the only ones to actually see this happen was the player and their Path Companion (and I suppose two sylphs as well, who were hiding and watching the events unfold in the Bowl of Embers from a distance).

But your idea definitely rings true - with Ifrit coming back stronger and stronger each time he's defeated and the Immortal Flames undermanned, it might be considered the 'least abhorrent choice' - better to sacrifice a few tempered victims than risk losing hundreds, even thousands, of soldiers to take Ifrit down the next time he's summoned.

And in any event, Thancred clearly feels empathy for it, but as is his personality, he bears that particular burden on his own (which probably went some way to explaining how Lahabrea was able to possess him later).