If I were to design an In Nomine CCG, I would start by tweaking the rules of Jyhad / V:tES because in my opinion, it has one of the most balanced systems. In particular, rare cards are just different or outright weird, not necessarily more powerful; you actually want less of them. Common cards make up 60%-80% of any good deck. And, Jyhad had a very strong political element. It allows several completely different strategies for winning, primarily rapid bleeding, manipulative voting, and direct combat. As such, it's one of the games closest to what most players of the RPG would like an In Nomine CCG to be like. Additionally, having been an early game and from WotC, a substantial fraction of CCG-interested people have at least passing familiarity with it. Thus, it's the most logical starting point.
Give each minion a number of Corporeal, Ethereal, and Celestial forces. Each minion can hold Essence up to their total forces (replacing capacity and blood). Replace clan with Choir and Superior. Instead of discipline cards, you have cards (including Songs) which require at least X of one or more types of forces, and may be limited to certain Choirs and/or Servants of certain Superiors. Rather than torpor, you have Limbo, with Diablerie removed. Change it so that instead of methuselahs, each player represents a Superior. Bringing into play Servitors of other Superiors should be slightly more expensive, such as adding one to the cost, and bringing into play Servitors of the other side should be prohibitively expensive, such as doubling the cost. The natural consequence of this is that you have mostly your Servitors, as well as some on loan from other Superiors to fill in specific needs.
The problem is that the objective in Jyhad is obliteration of your enemies. This only works for really dark In Nomine. An alternate idea is that all mortals (expanded from the minions of the original game) have a Destiny and a Fate. Then, you can take actions to help them approach one or the other. Once they meet one, you can score them, and the goal is to rack up X soul points first, with each human scoring as indicated. (Perhaps they have to meet either Fate or Destiny, and then be killed, if you feel grim, and, at least for the angels, a bit dark.) Fate and Destiny might be simple ratings, such as 2 and 3, which require that many Fate/Destiny actions by a minion, which would be directed actions at 0 stealth, similar to the bleed mechanic in the original, but targeted at minions (possibly your own, in which case it should probably be undirected), rather than at players. Alternately, a more complex Fate & Destiny system might have more specific requirements, such as a committing a sin or virtue, which can only be caused by a Celestial with some specific trait (either just Choir/Superior/Force rating, or yet another list of properties, such as "strong" and "persuasive"). There could also be generic people, played to a central pool and not under the control of any player, only there to provide targets for salvation and damnation (like the hunting grounds in Rage).
Votes would be for one side only (like the Camarilla/Sabbat distinction), representing the Seraph Council and the assembled Princes.
Additionally, Interventions need to be there in some form. If some mechanic required rolling dice, that could be the hook for them, but none does. There could be intervention cards, that you draw and use. Or, each Superior could have a set number of interventions (possibly different, if they have other powers to balance things out), which let them do something in the game, such as draw an extra card, untap a tapped minion, gain extra Essence, cancel another player's card, gain votes, or some such.
As to Discords, they could be like clan hosers, cards that can only be slapped on certain Choirs/Bands or Servitors of a certain Superior. If we want to include Dissonance at all, it could be some sort of counter that takes the place of Essence; you can't spend it, but it counts towards a Servitor's current amount of Essence, effectively lowering their capacity. It may be removable by some action of the Servitor's or through your (the Superior's) direct action, requiring the expenditure of your Essence pool.