Its better to have annonas be branching really low to the ground so you can reach the flowers. I would let both the branches grow and not try and have a long central trunk. Like 12-18 inches max on the main trunk of a annona tree where it starts to branch out or in 4 or 5 years you will regret it.
How far from the dirt are those branches? If you have to remove one, go ahead and do it now, it wont hurt anything. You could stake it up straight like was mentioned if you are going to only keep 1.