The similarity is a coincidence; these words are unrelated. Etymological dictionaries such as De Vaan's give the following account of the two words:
The earlier form of the conjunction cum is quom; this is attested in early Latin, and also in the word quoniam (< quom iam). It is descended from Proto-Indo-European *kʷom "when" and has cognates in other IE languages, including English when.
The earlier form of the preposition cum is com, which remains its form in compounds (com-). This is from PIE ḱom "with", which also has reflexes in other languages, including the Germanic verbal prefix ge-.
The Italic cognates suffice to show that the first sound of the conjunction was a labiovelar (Umbrian pumpe "whenever", with p from kʷ) but the first sound of the preposition was a velar (Umbrian kum-).