The Ancients had no idea what was happening, they wanted to put a stop to involuntarily creating abominations that were devouring people alive in the streets. I'm going to go out on a limb and say most people would jump at the first solution to that problem. :P

Also, the suffering part didn't even matter in the end. The Final Days still returned to Etheirys, and after 12k years the sundered were still unequipped to handle it. Had Meteion not been defeated, they would have had to flee into space indefinitely.