What is the ruling on praying with an Imaam who sits in the second rakah of witr and then does qunut after reciting the surah in the third rakah?
It is disliked to pray witr like Maghrib as comes in the Hadith
reported by Abu Hurairah [may Allah be pleased with him] that the Prophet (ﷺ) said:
لا توتِرْ بثلاثٍ تُشَبِّهوا بالمغربِ
Do not pray witr resembling it with maghrib
[Graded Saheeh by al-Albani in Kitab Salah at-Taraweeh pg. 85]
Praying witr in this form is the favored opinion of the Ahnaaf [the followers of the mathab of Abu Hanifa]. For more on the reasons why they take this view and the arguments against it, one can refer to Fath ul-Bari (3/325/326)
However, if the Imam is praying witr in three rak’aat like maghrib, it is better to follow him in the prayer.
Shaikhul Islaam Ibn Taymiyyah rahimahullah said:
“…However, these Ahaadith did not reach all the jurists. So, some of them disliked praying in three connected raka’at like the maghrib prayer as was reported from Malik, some of the Shafi’yyah, and the Hanbaliyyah. Some of them disliked witr in other than that [from] as was reported from Abu Hanifa. Some of them disliked witr in five and seven connected raka’at as was said by some of the Companions of Shafi’ee, Ahmad, and Malik.
What is correct is that if the Imam performs something from what has come in the Sunnah and prays witr according to a form from the mentioned forms, then the one praying behind the Imam follows him in that. And Allah Knows best”
[Majmoo’ al-Fatawa (23/56)]
So it would be better in that situation to follow the Imam in his witr, despite his opposition to what is better.
And Allah Knows Best
Faisal Ibn Abdul Qaadir Ibn Hassan