I went digging deeper and came up with the following. It may not be the kind cleaning answer you are looking for, but I did notice each berry has from 2 to 4 seeds. Perhaps you are not damaging the seeds, but instead separating the four?

http://www.easywildflowers.com/cal.ame.htm

Here is a link that might be useful: Beautyberry

Possible solution: I fermented the seeds with 4 days in a solutions of water. The berries rehydrated and became very swollen. It was then very easy to smush the seeds out without damaging them as the seeds are hard and the pulp is smushy like an overripe fruit. Not sure if this process of hydrating and dehydrating damages the seed, but it sure makes seperating easier (maybe if you had fresh berries this isn't a problem anyway though). I also tried fully drying some, but that doesn't make seperation any easier.

I collected some beautyberrys and just dried them out. Then I winter sowed them around January and they sprouted in the Spring. I have a nice little baby shrub now..about 2 years old. I didn't do anything at all to the berries except dry them out!

Thanks for your help ghoghunter!

I collected some fresh seed today. They are incredibly easy to seperate when fresh.