Agreed. The various scriptures would simply be reinterpreted to align with our current understanding.
Even if some scripture explicitly stated that aliens do not exist, the existence of aliens would not disprove, or even diminish the possibility of the existence of God. From the perspective of practitioners it would simply mean that whoever wrote that scripture misunderstood what was told to them. In other words, man is fallible, and easily forgiven for misinterpreting the word of God. I honestly believe that the arrival of aliens wouldn't even prove to be a minor speed bump for organized religion.
"He made us in his own image in the sense of our spirit"
"He is imperceivable and therefore He may take many forms" (I.E. when God was a flaming bush)
Or my fave, "He works in mysterious ways".
The church will adapt as it always has for millennias.