I can't add anything specific since I don't use PCA, but as a general R piece of advice, I'd encourage you to reframe your question @Amonda - it isn't that you need to get rid of NA values necessary, but rather understand how PCA handles missing data and go from there. It seems like you're treating NA values as a nuisance or bug, when they're very much a feature.
It sounds like you've got at least two avenues here so far:
It would be great if you could give both options a try, and depending on what you find, create a reprex (reproducible example) similar to what you had in your initial post. The reprex package would be helpful now that you're adding in potentially other packages, though. You can get some details here on creating reprexs.