While he should have never been sent off in first place, I have no doubt Bauza will start him again soon. Hopefully AFA will appeal as you said but I'm not crossing my finger for that. The likes of Neymar and Suarez has been sent off disgracefully when playing for NT and it's not like the managers will ignores those guys just because they got sent off. Dybala sent off was similar to Messi first cap sent off... stupid reffereeing.
So Messi was playing with not only a hamstring and groin injury, but also a hip injury. Which is why Alario went to the wings in the latter stages -- so Messi would not have to run so much. Dybala is amazing, and will start to be for us as well. No worries there.