So unless you're shooting in Production Divsion, it is an advantage to shoot a caliber higher than 9x19
Most of the time. If a shooter cannot control recoil sufficiently of a major PF gun, they may be better off shooting minor until they develop the necessary skills to control recoil. My wife's small and not athletic and she spent her first two years of IPSC shooting a Kimber .45 loaded minor. She can shoot just about anything now but there's no doubt she progressed faster with the sport not having to fight the gun.
Production Division was implemented pretty much as a 'shoot what you got' division. The USPSA has long had a problem with people showing up with Rugers, Sigs, and Glocks mostly in 9mm and not returning because they were at a scoring disadvantage to the major PF calibers like .40 and .45 used in Limited.
The intent of Production, therefore, is to provide a place for double action guns to compete equally. If Production was scored major and minor, that scoring issue still exists.
I understand your point about having the penalty of extra recoil shooting major PF loads agains the minor PF 9mm's, but IMO, that's less of a liability than being scored minor and competing against major.
Also, if you reload, you can always download a .40 or .45 whereas you cannot not always upload 9mm to major (SAFELY!).
...using a Beretta 96FS. I will not be returning with that pistol, I would be better off bring my Ruger P89.
Maybe not. I would make the decision based on which gun you shoot better. Rugers generally have absolutely horrible triggers and many aren't especially accurate (though usually good enough for IPSC) - you may find that the Beretta acutually works better for you even if you are shooting major loads but being scored minor. Berettas are popular in Production, likely second two Glocks. Rugers are pretty rare, at least at the clubs where i shoot.
You need to find someone with a shot timer and set up some stages and run them a few times with each gun. Compare your times and your points and see what actually works best for you.