modulegraph already knows where the import is done, and users of the library can use that information to make decisions. 

There's no need to make changes to either heapq.py or modulegraph.

For py2app I've made the choice to no be smart about inclusions and just try to include everything that may be imported because disk space is cheap these days.  I just exclude optional dependencies (in py2app, not modulegraph) when I've manually checked that it is safe to do so and the dependency is large.