I tried something kinda risky. I hope it works, and I need some advice on staying on top of it so that it doesn't ruin the gaming experience for my players.

One of my PCs backstory has him raised within a cult dedicated to chaos and undermining the organized systems of power. He's also a Fallen Aasimar who is struggling with his angelic link and is trying to figure out if he'll have a Come to Good moment or fall victim to evil. Out of game, the player has expressed willingness to bend his arc towards good, although it'll have to be organic. Another one of my players is an Order Domain Cleric, raised to be a good little boy of the Empire.

I set up the initial story so that the cult assigned this Aasimar to shake the Cleric's faith in the Empire and it's laws and values. The Cleric was already on this path, as he recently discovered an Empire cover-up of forbidden necromancy and was investigating how deep it went. The Aasimar is basically encouraging this Cleric down the rabbit hole and trying to encourage him to test his morals, and the Cleric hasn't yet figured out that this is happening. I intend to have envoys from the cult continue to contact the Aasimar with new missions that involve undermining the empire, although this does not necessarily mean he will be asked to directly mess with the Cleric, just to act against the Cleric's larger goals and ideals. 

So basically part of my party dynamic is built upon player to player deception. This will come out eventually through RP, and there is entirely a chance that the confrontation doesn't go well. I've asked the player playing the Aasimar to prepare for how he's going to handle this situation, going so far as to have him consider the possibility that the party won't trust him and will reject him, possibly through combat, and almost certainly forcing him to roll a new character. He's okay with this, and everyone at the table is good friends so I don't see there being too many problems out of game. I also feel that if I don't handle this well, there's a chance of the Cleric feeling like some trust between player and DM has been violated. 

I'm wondering if any DMs out there have experience with this kind of situation, and if anyone has advice on how to gently guide the game as it develops. How have you handled similar situations at your table? How do I organically offer tasks that might nudge my Aasimar towards good without him feeling railroaded? How do I prepare for the confrontation going south? Any other advice would be great.

Definitely speak to the PC of the Cleric as well. Make sure they're on board with the general idea ahead of time. I too like to create a little party tension from time to time - it helps reinforce why they're working together in-character.

From my experience if both players are interested in the RP side of it, they'll find a way to work it out. If it doesn't naturally go that way, have a backup plan: find some way they can be forced to work together. It's a popular trope in TV shows and movies that the two people who hate each other get stuck in a lift together and have to learn to coexist. Do that to the characters, just find your own version of a lift. ;)

In my last game the Ranger's past came back to haunt him and he was forced to steal an important personal item from the Cleric. She then found out and he spent a good portion of the session RPing the guilty conscience and trying his best to prove himself to her all over again. So it can work, if both players are happy to play off each other.

Thank you for the response! I plan to speak to him once he figures out what's going on. We talk most days out of game and he is still none the wiser, but as soon as he starts to suspect something is up we're going to have a chat about it.