It doesn't really matter thus far. Later on in the game you still can decide if you want to do Sabal's or Amita's plan. I switched a couple times so far and either way I had a negative reaction (eg. cities being attacked and people die). It seems so far, that the main plot doesn't change and those decisions only decide on what the prologue or epilogue mission looks like.
IAmita is more focusing on economics and Sabal on saving the culture of Kyrat.
After dining with Pagan in the very beginning, wait for him to return back to the table (around 15 min), and this will trigger the 1st ending
At the end of the game, you can choose to kill Pagan, this will trigger the 2nd ending
At the end of the game, you can choose not to kill Pagan, and go with Pagan to scatter your mother's ashes. Pagan will fly away on his helicopter, and you do not shoot the helicopter down.
At the end of the game, you can choose not to kill Pagan, and go with Pagan to scatter your mother's ashes. Pagan will fly away on his helicopter, and if you have an RPG or Grenade Launcher with you you can take out his helicopter, which creates a mini area, where you can loot his body (amongst the helicopter wreckage)
There are 2 secret endings, that happen no matter what and vary depending on the ally you sided with (Amita/Sabal):
Sabal
Travel to Jalendu Temple, the same temple you were tasked with destroying or saving in a previous Golden Path mission, to find Sabal’s scene.
Here you’ll witness Sabal putting subjects to death for turning against Kyrat’s national religion. This cutscene only appears if you side with Sabal and make him leader of the Golden Path.
Amita
Travel to the town of Tirtha to see how Amita gets labor. This scene can only be found if you make Amita the leader of the Golden Path by destroying Jalendu Temple.
Golden Path soldiers are rounding up children for slave labor in her opium farms.
Best Answer
There is no advantage to you at all. It might make you feel good you gave a person another chance though :)