In the common case, I don't think that the os.waitpid(0, 0) is the hot spot, but rather this:

for child in self.active_children:
    os.waitpid(child, os.WNOHANG)

It's called every time, and it's O(number of active children).

os.waitpid(0, 0) is only called when max_children (40) is reached. Also, I'm not sure why it's called without WNOHANG, because that means that we will block until active_children falls below max_children. That's an arbitrary limit, especially since it's not documented.

I've written a first draft patch using process group, that removes active_children and max_children.
The only slightly tricky part is the call to setpgid from the child and from the parent, to avoid a race where the child could try to join a stale PGID.
Note that I assume that setpgid is available on every Unix, since according to http://pubs.opengroup.org/onlinepubs/007908799/xsh/setpgid.html , it's "Derived from the POSIX.1-1988 standard".
Also, according to buildbots' configure logs, it's available everywhere.