the protocol calls for dilution of the liquid citricidal GSE, so although the taste is still bad, it is lessened. and gentian violet also has a taste of a sort, so either treatment could invite a nursing strike. not to mention, simply painting the treatment of either type could invite a nursing strike on its own. in my experience and my friends' experiences, it has been a short lived aversion and has rarely led to a full blown nursing strike.
personally, i would consider doing the treatment on both nipples and in baby's mouth in this case. it sounds like your instincts might be pushing you in this direction and i would follow that instinct. if you don't notice a change within a few days, consider stopping or trying a different treatment. again, in my experience, gentian violet helped us feel relief within a few days the first time around but not the second time, so we tried GSE and we felt relief within a day and a half. it's also great for bum rashes of a yeasty nature.
sending you pain free nursing vibes...
~claudia