Our first introduction to Dirk is via Bro, yes, but the idea that Bro is gay wasn't something that got given any kind of grounding until Dirk is introduced as a character.

Similarly, characters like Vriska weren't written through the lense of being trans when Hussie first penned Serket, so I don't ascribe the acts of violence that Vriska exhibits as indicative of Hussie viewing trans women as inherently more violent. I think a beautiful job was done to elaborate on Vriska's identity and smooth over those prior parts of her writing to veer away from any particular connotations towards a transmisogynist portrayal.

Bro wasn't a gay man when the story began, Bro didn't have a concrete identity until Dirk came in to existence to elaborate upon that identity. When I'm discussing Dirk now, I am focusing on his identity through the entire comic and not just one moment (despite also acknowledging how ideas and desires for those characters morphed through time.)

If Dirk never existed in contrast to Bro, to answer your question, yes, making Bro gay would be homophobic as fuck. But Dirk no longer exists in contrast to Bro; hence yes, it is just outright homophobic that the guy who is singled out by the story as explicitly gay MULTIPLE times gets penned like this.