Hmm, I think Utena is a direct contemporary: it was airing in 1997, and serialization/publication for Maria-sama ga Miteru started in 1997/1998 (not quite sure on if the 1998 refers to the first volume or start of serialization). I feel like Maria-sama ga Miteru is in a really weird spot with Class S: the author is an alum of an all girls' Catholic school and apparently based the setting and customs off her own experiences and only later read the classic works. They share visual motifs, but more out of shoujo lineage than direct inspiration. I don't think there was any Utena -> Marimite crossover, and similarly, I feel like there probably isn't any Onii-sama e/Dear Brother -> Marimite crossover, even if we look at the anime: visually, Marimite's anime is more clearly linked to its contemporary high school shoujo series than the extravagant and dark visuals of Onii-sama e, while Utena takes on a lot of visual influence in both the setting (the stain glass window, the bouncing curls...!) and, in particular, the direction--Ikuhara was a big fan of Osamu Dezaki's Rose of Versailles, and Dezaki went on to do the Onii-sama e anime, too.