They had to weaken Glory. It was something that worked last time, and it would allow for Shannon to come back to her senses again. Willow was the one in charge of the spell, but Giles was lending his ability as well, plus he was helping to corral Shannon as well. He didn't want her to get loose and try to join with Glory. Last time, all those affected had left to build the leaning tower of metal that had crashed a few months later (why no one had taken it down before then he had no idea). He had no idea what they might try this time.
He hoped this ended without any of them dying again, but he didn't have much realistic hope for that. Last time it ended with Buffy's death, and this time he feared the same, much less what might happen to Dawn, Connor, and all those fighting. He simply hoped that Glory could be weakened in enough time to truly prevent hell from being let loose upon this world.