Let me give you a quick timeline.
In May 1947's Wonder Woman #23 showed Diana in flashback having adventures as a little girl.
Twelve years later in April 1959's Wonder Woman #105 had a flashback tale of Wonder Woman when she was a teen. She was first called "Wonder Girl" here.
August 1961's Wonder Woman #124 kicked off a series of out-of-continuity "Impossible Tales" in which Wonder Woman appeared alongside the teen "Wonder Girl" version of herself, as well as a toddler version called "Wonder Tot", and her mother Queen Hippolyta, creating a "Wonder Family".
By Wonder Woman #150 (November 1964) the "Impossible Tale" label was retired, though Wonder Girl continued as a regular fixture in the publication, both side by side with Wonder Woman as well as in her own solo stories.
During this curious 5-issue period, Wonder Girl is no longer referred to as an "impossible" younger variant of Wonder Woman, however no other in-story cues explaining her existence are provided. Hippolyta does refer to them as her daughters, though and Wonder girl, Wonder Woman, and Wonder Tot repeatedly identify themselves as a family.
July 1965 had Wonder Girl continuing to appear appear in Wonder Woman comics while in the same month there was a Wonder Girl that joined the Teen Titans. There was not even a hint in either series that they weren't the same person.
November 1965, Wonder Girl (specifically the Diana) version was fired from the comic and retconed away in a rather tongue and cheek Wonder Woman issue.
July 1969's Teen Titans #22 Wonder Girl would be identified as Wonder Woman's younger sister, and was given the name Donna Troy.
"Never assign to malice what is adequately explained by stupidity or ignorance."
"Great stories will always return to their original forms"
"Nobody is more dangerous than he who imagines himself pure in heart; for his purity, by definition, is unassailable." James Baldwin
I feel like too much is always made of Donna's "accidental" beginning. It's a cute anecdote, but real Donna/Wonder Girl has been around since 1965 (arguably 1964), or almost 60 years. Imaginary tales Wonder Girl, who caused the confusion, was around for only 3 years.
But back to her best origin, you have a good point that we still have no idea who Donna's FATHER was. If the first origin is back in play (seems like it is)...there's still an untold tale there. For all we know, Donna's dad is still alive.
Trigon? Zeus? Emperor Palpatine? BATMAN??
"Never assign to malice what is adequately explained by stupidity or ignorance."
"Great stories will always return to their original forms"
"Nobody is more dangerous than he who imagines himself pure in heart; for his purity, by definition, is unassailable." James Baldwin
I think the point of the original story is that he was unimportant.... Her mom got pregnant, he obviously disappeared, and she had to give Donna up for adoption. It's mostly an all female- centric origin, like Diana's, but the addition of the Stacys ( and their return to Donna's world ) touches upon her ties to Man's world.