I believe that girlfriend and boyfriend originally were used for children who had a "special friend".
They were kinda like dating but too young to really do much than give each other a peck on the cheek and maybe talk about how they'd marry someday.
Since a lot of children kind of segregate according to gender, it would be somewhat common for a boy to only have one girl friend, and for a girl to have only one boy friend, and that would be their special friend.
I believe that later on, the term was used for adults either as a euphemism, or to "make fun" of the relationship and insinuate it wasn't serious or adult. Kind of a "baby" relationship, that hasn't yet developed into fiance or spouse.
Nowadays it's very common to date for years before getting married, and it's very common to date and never get married (even when you're with the same person(s)). But the term has entered common use so it makes sense to still use it since it's what other people understand.
Lover, on the other hand, being less "childish" in connotations, implies sex, which made it evolve for some people to mean sex only, which is obviously weird since "love" is in the word itself. As a result though, it still has some connotations of an affair or a partner you are not serious with but do have sex with.
I agree though that etymologically, lover makes more sense.
I actually know people who use "ladyfriend" instead of "girlfriend" to avoid the prepubescent undertones. Not sure if people also have a male adult equivalent.
EDIT: also, don't forget that while "boy" and "girl" now mean prepubescent children, it used to only mean unmarried males and females respectively. Probably another reason for them to be used for an unmarried relationship.