No.
Currently there is no way to take things out of containers other than as part of reactions that indirectly remove them (e.g. cooking, planting, drinking). Emptying containers destroys the contents.
I guess it might be possible to create custom reactions to take things out (something like a fistful of rye grain reaction that generates a fistful of rye grain removing it from a container). Note that this is a guess: I haven't tried.