I play the SC allowing me to roll 3 dice hittting an army with a 3+ in the same terrority. I score 3 hits directed at the army in Minas Tiriath. I can choose a captain.
1. I pick Faramir, but could I pick Gandalf?
No. Gandalf is a Companion, not a Captain. The Captains in the Gondor scenario are Faramir, Imrahil, Theoden and Eomer.
2. Also, can the hits be directed at the gates? rules state all hits against an army in Minas Tiriath are 1st taken against the gate.
In this case, the hits are applied directly to the Army. Per the FAQ, any card that is "directed" to an Army ignores Stronghold protection. If the card says something like "roll 3 dice and damage the Army on a 4+", the damage goes directly to the Army. If the card invokes a battle against an Army in a Region, the Stronghold protection would apply as in a normal battle.
"War is much more fun when you're winning!" - General Martok