Well Lithe, I'll take a stab at your little problem as one of my favorite things to include in the game is a bit of moral grey area.

1) You have to remember that most of the time, people will automatically assume that those that work against them in anything but the most passive ways as the "bad guys" and usually even the good guys will do something morally ambiguous in order to make things turn out in their favor. Think ends justify the means. Your "bad guys" could have been doing that. Possibly they have been attacking businesses run by your Patron and in the process have harmed innocent workers or customers. Your Patron just happens to leave out that the store was a front for a drug ring or something. Its less about what your Patron tells the party and more about what he DOESN'T tell them.

2) In order to keep your group from turning on the Patron, the best thing you can do is to keep the interactions with the "bad guys" on hostile terms. Even if they were to capture one to interrogate, keep the captive insulting and spitting in their faces or something. Even the most patient of people will lose it after a bit of that and strike the captive or begin to torture him. Another good point would be to make the party somehow be harmed by the "bad guys". A drive by shooting becuase the "bad guys" have found out the Patron approached the party to do some work.

3)Make the Patron play the part of the victim. Any interaction that the party and the Patron have should be with the Patron imploring them for help or being slightly servile. If the man is older it would help to play the helpless old man. If you are in a situation with the Patron's power showing, say it is simply a gathering of political activists or community organizers. Thinly veiled terms for Mobster, but good enough that, if played right, the Party won't catch on. A charitable organization would be a good cover too.

You can't

It is not possible for you to model the thought processes of God, no matter how much time you spend on it. There are too many fundamental barriers to emulating its mind, some of which you have touched upon in this question and in your previous one.

The silver lining here is that your players aren't in a position to do this either. Nobody, in the game universe or at your game table, is qualified to do this. So don't do it.

Don't play God as a character

God is a singular, primeval force. It will do what it does, and there isn't any reasonable way to explain, categorize, or justify any of those things in any true way. But that's fine. Humanity has been attempting to explain, categorize, and justify the actions of God for thousands of years, and the impossibility of it has never really stopped us.

God is a story. It's a story that you're going to tell your players, because that's the story that their characters are going to invent to justify the experience they just had. Something happened to them that fundamentally cannot be explained, and so they will paint over it and fill in the rough edges and do whatever they have to so that they don't all go insane.

There is never just one story

This encounter with God is not an objective event. It can't be. Every single one of the characters is going to fit their own story to what happens. Every single one of the characters is going to think they figured it all out. And they're all wrong. But they're all right.

You need a way to tell this story in multiple ways to multiple people at the same time. It's not going to be easy (I hope you didn't expect it to be).

1. Come up with a metaphor of God for each of the characters. This shouldn't be elaborate, but it's a lens through which you can craft the characters' unique experiences. Think about the varying manifestations of God in our world. These are all different people attempting to explain the unknowable. This metaphor will also probably suggest some human-like personality qualities of God; use them to further differentiate responses.
2. Come up with the intended outcome of the scene. This is where God is going to be steering the whole experience, and knowing about this goal will make it easier to improvise the events of the scene. You're going to be improvising a lot. This goal allows you to craft the story of this scene, which is really all there is to it. The rest is just expression.
3. Sit everybody down at the table. (If you're playing in some non-real-time format, this is significantly easier, but it doesn't sound like this is the case.)
4. Announce and enforce a very strict no-meta-talk rule during this scene. Everything your players say about the game must be in universe. If they want to coordinate perceptions, they're doing it explicitly.
5. Pass each of your players a card telling them what their character perceives at the start of the scene. This should map to each of their metaphors, but all of the descriptions should have similar themes (keep in mind the scene goal).
6. Let the players describe their characters' actions, and then write out how God responds to each of them. The response should be based on whatever any of the characters has just done, but each will see a different reaction. This is going to be slow, because you have to think about the responses and then write several of them, but that's pretty unavoidable. Remember that you are in some sense portraying a different scene to each player, but that the end goal is the same for all of them. This can get very slow, so simplify the communication as much as possible on your side: speak with brief, vague statements; use imagery rather than words; and don't be afraid of your signals being too subtle. All of these things contribute to the ambiguity of the encounter, which is exactly right.
7. Eventually, the scene reaches its goal, God leaves, and everyone can go back to however you normally play. Depending on how much you tailor to each character, their recollections of the scene could be very different, which is a good thing.

At the end of this, the characters have each experienced something very different, but the fact that all of their actions were interwoven consistently and that there was that single secret goal that you were working from should provide enough similarity for them to agree that something happened to all of them and that there's a direction to go next.