It's funny, but Alphinaud, in-story, once addressed this issue. I'm not sure exactly where he said it - perhaps to Ysayle herself - but basically, he acknowledged that even Louisoix himself resorted to primal summoning in his attempt to prevent the Calamity.

What's worth noting is that both times Ysayle transforms after she allied with us, she wasn't using up a source of aether that had been gathered for the exact purpose of her summoning. When she transformed against Ravana, she was essentially stealing his crystals. When she transformed at the Garleans, she was using her own Crystal of Light.

(Sure would be interesting if that turned out to be foreshadowing that we will eventually be forced to resort to the same thing with our own Crystals.)

Also, Thordan wasn't going to stop at just defeating the Ascians. He was intending to take over the entire world, (insert Saturday morning cartoon villain laugh here) or basically rule over all of mankind as an immortal god-king. To that end, he was trying to kill us, since as primal slayers, we were the first hurdle in that plan. Too bad for him, we ended up being the last hurdle as well.