Making it back to Castle Black in one piece, Jon is faced with a number of brothers none-too-happy with his actions. Thankfully, he has one friend, as always, in Samwell Tarly. The two have been through a lot together, and it is easy to see why Jon doesnt want to see him leave The Wall. However, he respects his wishes, and allows him to depart for the Citadel in order to train to become a Maester. What happened later may still have taken place with Sam there, but it certainly didnt help Jons case to have his closest ally - the one largely responsible for him becoming Lord Commander in the first place - leaving him, meaning he had very few friends remaining.