You can't. Either give up on getting Anima, or find a way to defeat the Aeons. You'll either have to train up loads, or pay Yojimbo a lot of Gil, and if you're lucky he'll use Zanmatto on them.
They are the dark Aeons. And they are TOUGH.
You should still be able to get into Kilika, Zanarkand and Djose temple, so if the items you missed are in there, then you are in luck.