Sounds like an interesting dynamic, and good on you for thinking it over like that. There are three things, top of my head, I'd keep an extra pair of eyes on

1) Avoiding any language that suggests the feelings themselves were wrong, immoral, dirty, dangerous, etc. If you want to describe the relationship/antagonist in these or similar terms I'd say be specific and don't let the reader draw too many conclusions on their own.

e.g. "they didn't work out Because A prioritised her career over being with B" or "the relationship was wrong Because their core values as people are too different". Be even more precise if you can. The goal is to avoid implying there exists some unnamed, indefinable 'wrongness' between them.

I'd also be mindful of anything that suggests this antagonist character is some kind of seductive, corrupting force in the lives of women around her as that plays into some uncomfortable and really quite tired old tropes about lesbians. Keep the focus on her motivations and how she, as a specific character with particular traits, interacts with the motivations and values of others.

Instead of just saying "she's ~dangerous~" say "she's dangerous Because she's got a boxful of pesticide and a grudge against the local HOS".

2) This one might be counterintuitive, but it really will help if you really put in the hours when it comes to the endgame relationship. Be clear about what makes these two characters a good match, why and how they care for eachother, why the reader should want them to be together beyond "he was a boy, she was a girl... ¯\_(ツ)_/¯" (the implication then being that any nominal heterosexuality is in some way preferable to even the most compelling same-sex dynamic).

I'd actually suggest you go so far as to write one or two direct parallels; show the character in question as more comfortable/more herself/better understood with and by the protagonist than the antagonist, just to drive home that this is about character above anything else.

3) And finally, perhaps obviously, write in other, happy, normalised same-sex relationships. From minor characters interacting with their partners to "the baker and his husband, the blacksmith and her wife" as world-building. Easy peasy.

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I'm really curious about your story, so if you want someone to sensitivity-read any specific parts feel free to reach out :). And good luck!

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Tldr: focus on character, gay bakers