Does Hera's power allow you to discard a hero 'reserved' by Zeus (using that Hero's power)?
One god's special ability cannot nullify another's.
So to answer your question, no, Hera can't discard Zeus' "reserved" hero.
Can you use Hera's power after taking the hero for this round (ie. once the track is refilled to 3)?
It is up to you to use Hera's ability at any time during your round. The difference will be
(as I interpret it) the positions of the 2 remaining heroes. So choose wisely