Remember that "lighter" Yuri is not that rare. For example, Shuumatsu No Izetta was not Yuri but is had undertones as subplot for the main protagonists.
There was also Ange Vierge and even that anime with Kokona and Papika that I'm forgetting the name right now, New Game etc etc only in one year. "Yuri" on a lighter tone is not that rare.
The thing is, those were not a serious confirmed Yuri series.
On the other hand, when things start getting real, people complain. Be it for the presence of males, or for the character of the girls not being the purest and perfect souls.
Whether we like it or not, Yuri is not meant to be a popular genre. It cant be as popular as the rest of shonen types of anime.
So NTR giving a bad name to Yuri is really not an issue imo.
And I seriously doubt how much of an appeal the male characters in this particular situation are able to have to attract a bigger audience. Their roles are not the type of male characters that appeal to the female otakus. It would make more sense that Fujiwara and Takeda would attract male audience with a "gay girl being with a guy" fetish instead.