I do not think Dave was a swipe at Bill Clinton at all. The film is primarily a modern update of The Prisoner of Zenda. In Zenda, the King has not yet been coronated when he is kidnapped. Two of his loyal retainers recruit a look-alike distant cousin - Rudolph Rassendyll- to impersonate the King. He meets Flavia, the King's betrothed. She is at first cold to Rassendyll because she has met her intended husband the king and finds him to be a drunken jerk. However, Rassendyll is more charming than the King, and is smitten with Flavia, and wins her over.
I'm sure the animosity the wife showed the president in Dave is merely an update of the situation in Zenda. The whole point of it is to create a doomed romantic triangle in which some get hurt, but all do their duty in the end.
Dave was a swipe at the "heartless" Republicans who didn't appreciate Dave's "jobs" plan.
The movie came out in May 1993 and the script would have been written some time before that.
The adultery theme is interesting in light of what Clinton got up to, but if the movie really were about Clinton, wouldn't the film makers have made their president more folksy and good ol' boyish?
I wonder if The American President two years later was really about Clinton, though -- a defense of his behavior against the puritanical Republicans, which turned his adultery into a widowed president having a girlfriend.