Where can I find "food safe" glass marbles for sous vide cooking?
I would recommend using Whiskey Stones. They are used in whiskey instead of ice cubes. So they should be heavy, won't rust, and are supposed to be immersed in liquid that you'll consume. I think that probably meets all your criteria. 

Whiskey Stones


Another alternative is to use a rack. This comes with the Sous Vide Supreme and I find it quite useful for keeping meat submerged. It does however only accommodate certain sizes of meat. It works quite well. You can buy it separately online for $12.