What should I do if I am led in prayer by someone performing the Witr prayer, who then begins the Qunut supplication? Should I discontinue my prayer or follow him in the Witr supplication?

The preponderant opinion is that it is valid for someone performing a fard (obligatory) prayer to pray behind someone performing a nafilah (supererogatory) prayer. They cite as evidence what was narrated by Jabir that Mu'adh ibn Jabal used to pray the 'Isha (night) prayer with the Messenger of Allah, then return and lead his people in that same prayer. If the Imam's prayer is Witr and he performs Qunut therein, it is preferable for the congregant to follow him. However, he may also intend to separate from the Imam and complete his prayer.