Let Pagan Min go. He's pretty much the only person in the country that likes Ajay and has no ulterior motive with him. He doesn't use him as a propaganda mouthpiece, to win any wars, or anything. He just genuinely cares about Ajay and Ajay's mother. Plus, he gave me Kyrat.
After Yuma's drug trip, Ajay no longer trusts Amita... but he never trusted Sabal's intentions in the first place. Between turning the country into a narco-state and a conservative hellhole, Ajay was stuck between the two, but here's an opportunity to finally tweak things to my advantage.
First, Bhadra asks you to make a choice between the two, and I choose Sabal, not cause I actually want her to be the whole Kyra reincarnation thing, but because it's part of Ajay's gambit. Plus, Bhadra is safe cause Sabal won't try to killer (I know Amita has Bhadra killed in her post-ending). So with Bhadra "safe", I take down Amita's support and exile her from the country (but don't kill her).
Afterwards, we take the fight to Pagan, battle up his mountain, and then negotiate with him. After Ajay finally puts his mother to rest next to Lakshmana, I allow Pagan Min to go. Killing him serves no further purpose and he basically did just name me his heir.
Afterwards, Ajay walks back down the mountain to discover Sabal about to commit his purge. This confirms my suspicions about him and I put two in his head.
Kyrat now belongs to Ajay Ghale, who is the only one out of all the cast that has a shot at giving Kyrat a good future.