Yes, "Ghoul Touch" allows a saving throw to avoid being paralyzed.
The "Saving Throw" entry in the spell description usually refers to the main effect of the spell, unless mentioned otherwise. If only part of the spell were to be negated, there would be a text like "Fortitude (partial)", or something. The rest of the text handles the additional effects, if any. For example (i just opened the PHB randomly): "
Bane"...
In the case of "Ghoul Touch" i'd say the target should do 2 Fort saving throws: the 1st to avoid the spell effects altogether, the 2nd to avoid being sickened.
EDIT: typo
EDIT 2: The general rule for STs can be found in PHB p.176-177