It is an old and outdated expression. It's used nowadays only as a joke, much as someone might say "Prithee, fair maiden, woulds't hie with me to yon Dunkin' Donuts and quaff a flagon of coffee?"
It would typically have been used when a man and a woman, in a sexual relationship--perhaps living together--got married, perhaps because the woman had become pregnant. The societal view was that the relationship was sinful, and especially shameful to the woman. But if the man "made an honest woman" out of the woman by marrying her, society could forgive and forget.
I _think_ "honest woman" did not mean "truthful." I think a prostitute would have been a "dishonest woman" and a married woman would have been an "honest woman."