I believe Fritzing is written to use only one processor so some things just take a loooong time. OR at least that is how it looks on my system when I monitor CPU usage. I think this means that the user interface and the calculations are on the same thread so we get the unresponsive pop-up. If it used two threads, one for the interface and one for the calculations then it could give us proper feedback of its current state.
I would attempt to change it if I was a programmer but unfortunately I am not. I know my way around but I know nothing about GUI programming.
I have even failed trying to compile the development version of Fritzing on Linux so even if I was able to make changes I couldn't test them.