This does sound fun. Some things you need to consider. Also I'm a little tipsy so if this is crazy crazy, just slap me across the face and tell me to wake up. :-)
Can Heroes fight the other team of Heroes?
If so, probably some adjustments like like this would suffice:
If a Hero ends her activation in the same space as Heroes in another faction, she must fight each of the Heroes in her space. (Faction to fight first is activated Hero's choice, order within faction is Defender's Choice. Fight zombies last because they're slow.) If both parties agree not to fight, no fight occurs. Exchanging items is only possible if both parties agree.
After the Zombie movement phase, the Zombies fight all Heroes in their spaces but instead of splitting up evenly, get to fight each Faction separately, and get to decide what order to resolve Factions (as a whole, for simplicity?) The Heroes within the Faction get to determine the fight order within their Faction's defense phase.
Any card that targets Zombies, such as a ranged weapon, may be used to target another faction instead, but not both at once (and not more than one faction at a time except for ranged weapons, since it makes sense - i.e., the pump shotgun could fire at anyone in a space regardless of their affiliation.) Any card that targets "all models" in a space, however, still targets all models in the space.
"The Hero Turn" includes all factions. (Decide a rule on what order the factions take turns in.) However, Becky's Heal ability takes place at the end of her Factions activations (that way she has a chance to heal her party members before all the other factions can wipe them out.) Cards like Bickering and This Could Be Our Last Night On Earth only affect members of the same faction in the same space.
Zombie Victory Condition of killing 4 Heroes needs to be replaced.
Hero condition of surviving until sunrise/etc needs to be replaced (all the factions can't win.)
When the an empty Hero Deck is discarded from, this would still be a Zombie victory condition and would cause all the Hero factions to lose together (there's nothing else left in the town to help them!)
Depending on the Scenario, it might be worthwhile to introduce the concept of Nonlethal Damage from unarmed Melee attacks and blunt Melee attacks (i.e. not involving blades/saws.) A nonlethal damage would be indicated by putting a yellow XP token into an empty wound spot instead of a normal wound marker. If all of a Heroes wound spots are filled: If they are all wound markers (red) they die like normal. But if any of them are yellow, instead they simply fall unconscious. Any regular wound will replace a yellow wound (if any) any time it is dealt. An unconscious Hero attempts to roll 6 on a D6 during each of their activations in order to wake back up (remove 1 yellow wound to wake up.) Any hero in the same space as another Hero may also attempt to roll a 6 on a D6 once during their activation to wake up the unconscious hero in their space.
This would allow you to slow down the other team without being murderers. Zombies could still easily come along and finish off any who are left unconscious, though!
Ok, I'm getting crazy here... carry on!