For RP purposes, Thrawn does not respect Kallus. As the show goes on, though, Kallus can be a grave threat to Thrawn because Kallus is INTELLIGENCE – which is basically like the “Waffen-Shutzstaffel” for the Empire.
ISB get their targets. Thrawn is smart enough to outsmart Kallus completely, but it would make it very hard for him to shut Kallus down from his investigation. Intelligence is cruel and back-stabbing is frequent. Ysanne Isard is primary proof of that to what she did to her father, Director of ISB, Armand Isard (source).
There are 2 ways this can go for Agent Kallus:
1. He abandons his post and joins the Rebellion, which is something fans do when the LIKE a character and personify him too much. Kallus abandoning the Empire and its resources of which his character trait is not prepared to DIE to run off and join the Rebels seems far-fetched and weak-willed. Kallus is military. He believes in those set of values. He’s trained all his life for it. To give it up would be delusional and he would die because of it.
2. He follows Thrawn as the new “Gilad Pellaeon” and completes tasks that Thrawn will do as long as he lives. They both learn from one another and exact the will of the Emperor across the galaxy. Easy.
Now, the entire collapse to this is a surprise additional characters of the plot:
One being Mara Jade. How that plays is up for contention. Will Mara Jade be returned to canon? Possibly.
But not without others. Such as Natassi Daala, Ysanne Isard and Rae Sloane.
Natassi Daala is Tarkin’s babe. She runs ships.
Ysanne Isard is just plain evil and it’s amazing the fanboys have not advocated for her since they’d make her like someone we know right now IRL. Easily.
Rae Sloane is the measure sense of rationality and Vader likes and respects her. So does Thrawn. Which would make her the most amenable to adding in Star Wars Rebels.
Ysanne would be the best villain overall, wrecking havoc across the galaxy.
But if the LFL story group does as speculated, they need another huge villain group to justify the brutality to the Rebels that drive the Rebels to these risk-taking missions, i.e. stealing the Death Star plans; goading the Imperials; and several other activities.
In the end, Kallus will have to help the Rebels in a risky mission to help someone he cares for. At the end of the day, our speculation is, he will stay at that location, safely.
OOC: Really Kallus?