The show doesn't ignore Sheldon’s germaphobia; it acknowledges it and shows him moving past it because the person matters more than the "messy mixing of bodily fluids".
The true "excitation" of the episode isn't the sex itself, but Sheldon’s . Episode 11: The Opening Night Excitation
The return of Bob Newhart as Arthur Jeffries (Professor Proton) in the form of a "Force Ghost" serves as Sheldon’s subconscious moral compass, pushing him to realize that "being with [Amy] is more important" than a movie. The show doesn't ignore Sheldon’s germaphobia