Can I target Baron Nashor with Iron Balista?

No, you cannot target Baron Nashor with the ability of Iron Ballista.

According to the card text for Baron Nashor, it has the ability: "I can't be chosen by enemy spells and abilities."

Iron Ballista's ability reads: "exhaust : Deal 2 to a unit at a battlefield." Because this ability requires you to select a specific unit to deal damage to, it constitutes "choosing" that unit. As established in RiftJudge FAQ #8771, when an ability requires selecting a specific game object, the word "choose" is implicit, and Baron Nashor's protection prevents it from being a legal target for such effects.