As described here the characters on Gilligan’s Island represent the Seven Deadly Sins.
The Professor = PRIDE
Mary Ann = ENVY
Ginger = LUST
Mr. Howell = GREED
Mrs. Howell = SLOTH
Skipper = GLUTTONY and ANGER
Gilligan represents Satan.
So it’s very plausible that both Ginger and Mary Ann get knocked up. Excluding Gilligan, since that presents a Rosemary’s baby situation, I would guess the Professor would be the father of both.
The Skipper and Mr. Howell are probably impotent, and I doubt the Skipper’s sexual preference would interest him in the farm girl or the bathing beauty.