I just got killed by her and when I went back to the Hive she was gone. Is the only way to get another crack at her to make an Abeemination?

Yeah, even though I'm playing a small world I just found a 2nd. Of course since they got rid of the obsidian requirement making an abeemination is REALLY easy.

Thanks. :D

I had that happen once but don't give up just yet, they can be hard to find. Now when I start a game I make sure there is a large jungle biome before I go any further just to make sure I probably have a hive around. While I could care less about the Queen, I want that Witch Doctor moving in as soon as possible.

It's theoretically possible, but I've yet to actually experience it myself ever since the hive mini-biome was introduced in 1.2. You may need to use a map viewer to find one, as I have experienced the available hives all being hidden from the easily accessible part of the jungle.

From what I understand, the only way to fight a Queen Bee again after challenging it in their hive is to make an Abeemination. If you've combed your jungle and found all the hives that existed, then it is the only way.