Can a related paper cover the non-thesis master disadvantages for applying for a PhD?
I would recommend the independent research avenue because I always believe you should do the things you enjoy most. It shows strong interest in your future field and you will be better equipped to get your love for the field across when applying for a PhD/other.

Things to consider when making the final decision are: 


How much the non-thesis masters is valued in the US compared to the thesis one? 
The availability of the supervising Professor B
Your certainty in applying for field B.
The requirements wrt the masters listed on the websites of the universities you will apply to. 
The genuine likelihood of publications in your independent research into B
How much you dislike supervisor and topic A.