I hear you. Crosstalk between related, similar concepts can be a killer when doing SRS studies. You can see my lamenting this here. My concerns are not quite as difficult as yours, but there’s a few tips there that might be useful for you. I come to WaniKani after having done Remembering the Kanji years ago using Anki. In it, you learn what kanji mean without readings or vocab. Kanji aren’t words, they’re concepts. And they don’t always map directly to one (or several) English words. Think about English prefixes and suffixes. They’re groups of letters that clue you into a concept when building the word, but aren’t generally words themselves.
Unfortunately, the concepts represented by the Kanji also don’t map to single pronunciations. Unlike an English prefix (like, post-, for example), there isn’t just one way to say them because they’re concepts borrowed from Chinese. So the kanji readings stem from retrofitting them to Japanese words.
WK tries to separate learning the kanji with a single sample reading from learning vocabulary that use that kanji. But it’s only a few days to Guru a kanji, if you’re keeping up with your reviews and add lessons as soon as they show up. Note that the first levels are sped up so after you finish those, it isn’t as bad. And a few levels after that, you’ll be busy with reviews and won’t be adding lessons the moment they become available either, which will also help.
Good luck!