IMHO no it wouldn't be homophobic.
Here is a sort of reductio ad absurdum example.
Imagine a story set in a Middle Eastern city in the 13th century (1201-1300) with a population manly Sunni Muslim, with minorities of other Muslim sects, eastern Christians, Jews, etc. The language would be either Persian with Arabic minority or Arabic with Persian minority, etc. And there might be merchants from distant lands.
So a rich merchant or noble has a large mansion with a large harem containing his mother, his unmarried sisters, his wives, his concubines, his unmarried daughters, those of his sons not yet old enough to move to men's quarters, female servants, mostly slaves, eunuch servants and bodyguards, mostly slaves. There could be dozens of people living in the harem, all female except for the eunuchs who used to be men and little boys who aren't men yet.
None of those people would be legally entitled to have sex with anyone except for the master of the house, but each of them would have various personal relationships with everyone of the others. And possibly several of them would have romantic desires for other members of the harem, possibly including sexual desires.
There could easily be an eternal triangle involving three female members of the harem, or even a more complicated geometric figure, while still involving only a minority of the females. And possibly one among the eunuchs as well.
And out in the city among people who live in small, ordinary households there can be many characters who have all sorts of relations with the people they know, possibly including various eternal triangles among members of the same and/or different genders.
And then the Mongol army arrives and besieges the city and breaks down gaps in the walls and the city surrenders. The Mongols herd all the people out of the city and at a signal the Mongols massacre everyone, including all the "straight" and "queer" characters in the story.
Readers won't get the impression that the writer is homophobic, more like the writer is Mongolphobic and want the readers to be Mongolphobic.
You may have heard of the Emperor "Elagabalus", who, according to the ancient historians, was really, really "queer" and was allegedly killed for it. "Elagabalus" is the main character in the novels Family Favorites (1960) by Alfred Duggan and Child of the Sun (1966) by Kyle Onstott and Lance Horner. And as far as i remember "Elagabalus" is depicted in those novels as both "queer" and a sympathetic character or even the protagonist, murdered by homophobic and/or power hungry characters. So the example of those novels show that it is possible to write stories where the "Queer" characters are killed off without being homophobic.