Archer alludes to the creation of the Prime Directive when he decides that he shouldn't interfere with the Valakians by giving them the cure. However even if the Prime Directive was in existance at the time, the non-interference aspect would not apply in this case, as the Valakians had already developed space flight and had contacted two alien races, so it was they who sought out contact with alien races. Even if the Prime Directive had applied to the Valakians, the damage would already have been done by their contact with the Ferengi and others.