Is there a gameplay benefit from siding with either Sabal or Amita? Or does the decision I make have no impact except on the plot of the story itself?
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.
While Ajay might have been fighting to keep Kyrat from turning into a forced-labor drug state, it would seem that putting his faith in Sabal's "traditional" beliefs may have been a regrettable choice.
After the fall of Pagan Min, Sabal's leadership becomes nothing short of religious fanatacism. He forces Bhadra into the position of Tarun Matara and publicly executes anyone who stood in the way of his quest for power.
Despite Ajay's desire to see a more progressive and modernized Kyrat, it seems as though Amita is more concerned with preserving her empire than the actual well being of the Kyrati people. After the fall of Pagan Min, Amita's Golden Path begins forcing villagers into labor in factories or drug fields and forcibly drafting children into their armed forces. As Sabal says in his parting words to Ajay, Kyrat has become "A land of equal opportunity where everyone's a slave."
Balance of power M1: Chose Sabal. Lives over information, unless you know what the information could be about. Choosing to let everyone die at the post for some information that could POTENTIALLY be useful isn't worth it.
Balance of power M2: Chose Amita, saved the drug fields. Gotta make money somehow, even if it's through such means of drug trade.
Balance of power M3: Chose Amita, destroying the factory would be counter productive to M2.