it only removed the Daleks from the medusa cascade incident

EDIT: Okay, actually it is your question that is flawed.

The crack isn't "Swallowing" things up, actually, what it is doing is REWRITING the history of the universe.

in the case of the crash on the Byzantium, with the clerics, it merely re-wrote history to remove the excess clerics from ever existing.

in the case of "Journey's End". It merely re-wrote history so that even NEVER HAPPENED. Just like the Giant CyberKing.

and it's the Re-writing of those things, that "feeds" it.