I've done this. My son didn't really have any issues with me swabbing his mouth out. Make sure it's diluted, it's been a long time and I can't remember what concentration I used. I also swabbed my nipples with it, cut sugar out of my diet and took acidolophous(sp?) to help thing along.
Having taken GSE orally myself, I could not would not do that to a poor little kid. The stuff is AWFUL. But I put 10 drops into water and drank it down, to help my own system get rid of it.
DS's thrush was blasted by four days of once daily application of Gentian Violet to my nipples. I will admit I haven't tasted it, but I put it ON my body, and unless the skin is open it doesn't hurt, and clears things up nicely. (on broken skin you end up with a temporary purple tattoo). Anyway, on the nipples once a day, for four days cleared him up right as rain.
It just took longer for me, hence the GSE in water...bleah.