How do I prevent two different guild tables from merging?

This is a problem for me too (raiding with multiple chars), and here are few suggestions :
Detect guild name (Id) based on current player and filter list based on that, but allow on class selection screen for guild to be selectable so we can check dkp in any guild from any char.

This one is quite easy to fix
Go to the MonolithDKP.toc change SavedVariables to SavedVariablesPerCharacter
Now you have support for multiple guilds/characters