Can the sunnah of the morning prayer be omitted in order to join the congregation?

Among the sunnah prayers, the two rak‘ahs performed before the obligatory morning (fajr) prayer are the most emphasized. This is because there are statements from the Prophet (peace be upon him) regarding the great virtue of this prayer that have not been said about other voluntary prayers. The Prophet (peace be upon him) said, “The two rak‘ahs of the morning prayer are better than the world and all it contains.” (Muslim, Salâtü’l-müsâfirîn, 96 [725])

It is generally disliked (makruh) to perform a voluntary prayer once the iqamah for any obligatory prayer has begun or when the imam has started the prayer, and one should join the congregation. However, due to its great merit, the two rak‘ahs of sunnah performed before the obligatory morning prayer are an exception to this rule. (Kâsânî, Bedâ’i, 1/297) If possible, one should not miss out on this virtue.

Accordingly, if a person thinks they can catch the last rak‘ah of the obligatory morning prayer with the congregation—or according to some opinions, at least the tashahhud—they should perform the sunnah. On the other hand, if one fears that by performing the sunnah they will miss the entire obligatory prayer with the congregation, then they should omit the sunnah and join the congregation. (Ibn Maze, al-Muhît, 1/448-449; Ibn ‘Abidin, Radd al-Muhtâr, 2/56)

Source: T.C. Diyanet İşleri Başkanlığı, Din İşleri Yüksek Kurulu