Is it permissible to seek refuge in Allah from Satan, the accursed, when getting up for Fajr prayer, in order to prevent the whispers of Satan and abandoning prayer, and to make it a habit?

There is no harm in seeking refuge with Allah from Satan upon waking up, especially if a person fears the whispers of Satan tempting them to sleep and miss the prayer. Indeed, remembrance (dhikr) is encouraged upon waking. Nevertheless, adhering to the prescribed (ma'thur) remembrance is more paramount, and one should not persist in unprescribed (ghair ma'thur) remembrances as one persists in the prescribed ones, lest what is not sunnah be made to resemble the sunnah, which could then be feared to be an innovation (bid'ah).