The fact about how your readers are talking about the lesbian relationship instead of the main mystery plot may be also caused by the fact that readers tend to comment on fun, simpler, and catchy things. They most likely do fully notice the whole mystery going on, but they just don't comment on it for some reasons. Probably they have theories, but think it's silly so they never said it. Probably they want to analyze a character, but they're worried to get it wrong. Probably they just remember an unpleasant feeling of having to do book reviews having to dissect the theme and choose to comment on the shipping instead.
You only know what on a reader's mind by their comment, and it's only a small fraction. You don't even know what's in the mind of those who don't comment. I feel like it's a waste to stop writing because of that. I don't get shipping but it's fine as it's harmless fun. Unless someone is starting to get harassed or sucked into a conflict which is also a cause many people quit a scene.
Also you can't control what readers think (unless you want to be a dictator author). Plus, part of their perception is shaped by what we write, and how we conveyed it. Maybe it comes out differently as being perceived by most other people, than by us.
It reminds me of a person who discouraged people to like their villain. No, I don't want your shitty projection protagonist, so I pick the one who make them suffer. Thanks.