Let’s let bygones be bygones and just make peace with this.
I can't make up with her that quickly.
How did Koichi bring about a reconciliation between the Mario brothers?
When you fix a relationship you are going through reconciliation.
The readings are the kun'yomi readings. For 仲 you're fine. That's what you learned with the kanji. For 直り think back to the vocab word 直る. That's what's going on here.