It seems to me that with the calligraphy tool it is unlikely that you would ever need every stoke of the brush stored as a seperate object since doing so makes a drawing unncessarily complicated.
I'm not sure about 0.45, but in 0.46 you can hold Shift to automatically add to the previously select object when using the Calligraphy tool, but I need this so often that it's impractical to always hold shift.
So I wanted to propose that a option is included on the tool control bar to allow you to toggle the automatic union or not.
A toggle could also be included to allow automatic differencing, which would create the effect of using the calligraphy tool as an eraser.
This is a mockup of the toolbar with the three modes (normal, union, difference):
