So, first of all, I really like the idea, so don't think any of what I say is to bash it, but to improve it
You would start out with easier FGs (Ferox) and progress to harder ones (Divine Glory in the end?)
Well, "harder" and "easier" are relatives. RoL/Hope beats Divine Glory's a** like 90% of the times, while Ferox is a pain because of his great healing capacity. I personally haven't won to him yet with my RoL/Hope deck.
Anyways it's true that there are overall "harder" FG's, so it could be a chance of doing something about that. Also, you could choose what god to attack first, so, problem solved!
You could have some idea what FG you would be fighting next, perhaps, so to avoid making that too easy, the ability to modify your deck at each campaign step would be somewhat limited.
Well, have you seen majofa's topic (
http://elementscommunity.org/forum/index.php/topic,13074.0.html)? It says what deck would work better against every FG. It's not final that those are the "best" decks, but they are mostly (I'd say 90%) great, and all of them have 50% win rate or more.
That would be a hard problem to solve, so I guess FG's shouldn't be the "final bosses", but the mechanic should be different somehow.
Given the % of wins against some FG's, completing the campaign (and conquering the Elemental Plane) might be very rare. Maybe it should be very rare, but if it's too hard, you could tilt the odds with the campaign bonuses ... (maybe get the option of 3 free Deflagrate against Octane, for example, if you've already taken Divine Glory's domain. Etc.)
As I said, given that you know which FG you're grinding, it wouldn't be that difficult. I guess the way to go would be making new, harder decks (the FG's aren't hard because of their decks, they're hard because you don't know which of them you'll be fighting, so making a counter to ALL of them is really of hard, as all decks skip at least one god, not to mention double hp and all that).
I say make your idea something more "solid", but beware of making it something that imbalances the game.