It's a thorny issue, but I don't think the lack of a qualification round makes a lot of difference: that girl, had she played a qualification round, would very likely have qualified, as the top boy and girl in each year go through. Most of my girl qualifiers have been the only girl entrant in their year group; the cohort where I've usually had more girls is actually the only one where a girl has ever come out top.
Part of me totally agrees that we shouldn't need gender segregation; part of me thinks that we have to do something to encourage the girls.
The thing I found to be different this year was that, at our megafinal, the year 6 boys and girls were playing together - when my year 6 girl went before, she was just playing girls, and finished a bit below halfway. This year she had got 16 points in school, but in the megafinal lost every match. Fortunately she remained positive and was happy that she'd put up a good fight in some matches. I've had one or two children pull out of the megafinal partway through because they were not enjoying being demolished, so I now tend to warn weaker players who have qualified "by default" that they should be ready for the possibility that they might lose most matches - this perhaps particularly applies to girls where they are mixed at the megafinal, but of course we don't necessarily know that until they get there.
As far as your suprema goes, she will presumably be aware that she has got through without winning any matches, and may decide that the gigafinal is unlikely to be much better. That might, of course, depend on whether the other supremas in her age-group are in the same position. If I were her, I think I'd have a look at the other megafinal results before deciding whether to go!
Her qualifying does not affect your boys qualfiying - in fact, six of the boys in the competition will have gained a point through playing her, so if anything she increased their chances of qualifying.