migrate_config only complain about keys not from defaults

has_option seems to return true if a key is found from defaults even if it isn't overridden
in a given section (ours was complaining about 'confs' in a a mostly empty junit-run section).

This seems to fix it, though in the event a section was actually overriding a default,
just with the same value, it will ignore that. I couldn't figure out how to see if a section
actually defined a key without poking around in ConfigParser's private fields.

Reviewed at https://rbcommons.com/s/twitter/r/1451/
Sync of https://github.com/pantsbuild/pants/commit/b981e4262b8d2b746da9badd8d26efdb441fed35