I'm not saying that every Ennead should be converted this way (that'd be alot of villain decks for one theme), but the 9 god team seems like it'd be a natural fit to take 5 or so of them and make versions for the new format introduced with Vengeance. They're already allied and can draw on multiple aspects of Egyptian mythology for their powers and abilities, and the Shrine of the Ennead could be made as an environment in and of itself.
I doubt that's likely to happen... perhaps we'll see some of them appear in the upcoming Villains expansion, I haven't had a proper look at the list... But in the meantime, here's a completely off the top of my head, absolutely untested, and presumably completely unbalanced, and possibly outright broken way of playing the Ennead in the way you suggest (Vengeance rules, Shrine as environment).
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Lay out H heroes, and H of the Ennead villains, alternating round in Vengeance style. Take the rest of the Ennead villains and place them under the Shrine of the Ennead card, before the first player; this will take the place of the Environment deck. Place the Ennead deck in the centre of the table; this deck will be shared amongst all villains and the environment. Leave room for a discard pile; this will also be shared amongst all villains and the environment.
Play in standard Vengeance style. Any references from the villain deck to start/end of the villain turn apply only to that villain. Other Ennead villains do still fire their effects based on symbols played in other villain turns (but see below about the Ennead members from under the Shrine). Any cards drawn from the shared deck on a villain turn (except where a card's effect specifically requests an environment card be played) are considered villain cards.
When the environment turn comes around, first resolve any start-of-environment-turn effects, then play an Ennead member from under the Shrine (if available), then play a card from the central shared deck (following rules below), then resolve any end-of-environment-turn effects. Here's where the key changes are:
- Any reference to cards from the villain deck on environment cards should instead be read as referring to cards from the environment deck, and vice versa.
- Cards played during the environment turn will considered environment cards, and will not be considered villain cards (excepting where a card's effect specifically requests a villain card be played). Ennead members from under the shrine will be considered Environment Character cards, and not villain character cards, for example.
- Environment character cards fire their abilities based on symbols on cards played as a part of the environment turn (or cards played due to the effects of environment cards), but their abilities do *not* activate from cards played during villain turns (or cards played due to the effects of villain cards), and vice versa.
- Yes, this means the Ennead is acting as two teams who may attack each other, and yes, this means that player abilities that target villain or environment targets will be limited to targetting the relevant team.
You win when you defeat all the Villain characters. You do *not* need to defeat any of the Environment characters.
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If this is too easy (I suspect not), treat all villain targets as having a maximum/starting health 10 higher than show on the card. For advanced mode, all cards fire based on symbols regardless of where they were played (Environment target's effects fire when villain cards are played, for example).
You can throw any Ennead Villain into a Vengeance format fight, just remove Shrine of the Ennead, Taste of Immortality (2), and Rise to Power (2). Treat (H) as 3 no matter the number of heroes.
The Ennead cards tell the highest, lowest HP Villains to act, so the Ennead Character acts as a support style character. It can be nasty, worst we had was Elemental Storm when Fright Train at +2 damage was almost dead. 9 damage to all hero targets hurt.
I know this isn't what you are posting about, but it really works well.
aawood, maybe you could pull the environment Ennead members out face-down, so their incapacitated ability becomes the environment effect.
I like that idea, much simpler that mentally reconfiguring the card text and such! 
Thanks for that suggestions. I'll have to give those a try.
If you have H Ennead acting as villains and their deck being used during both their and the environment's turn, what happens when it plays one of those "bring out another member of the Ennead" cards (Taste of Immortality, Rise to Power)? Would they just enter play as an environment card even if the card that brought them out was played during the villain turn?
Oooh, good question!
I'd probably go with that suggestion, of them appearing on the environment side as environment cards (especially if going with Trajector's idea about having them face down). I guess the alternatives would be to say that any such cards would be moved to the bottom of the deck and then a new card played, or to say that it simply acts as it would if no members of the Ennead were left to be brought out.