So, then, she goes to Avalon. What's the problem?
Yeah, but those spirits are dead already. And, further, copies of them still exist in the throne. Except for Saber, of course, who if she is killed just goes back to her body with all her memories, which really means that she wasn't killed at all.
Yes, she has. She died 1500 years ago (well, if you discount the whole "going to Avalon" thing...).