Gentian Violet is extremely damaging to the ears/hearing cells. I would not use gentian violet on an adult, much less a baby. Any of the gentian violet systemically absorbed can damage your baby's hearing. Look up "Gentian Violet" and "Ototoxicity" for more information.
In response to Lori from McKinleyville, CA regarding mercury in Gentian Violet. Angela from Vancouver Island posted this link: http://www.ec.gc.ca/mercury/EN/cstudy.cfm because she wanted readers to see the toxicity of mercury. You can confirm that Gentian Violet contains mercury on this site: http://www.ericsissom.com/health_alternative/mercury_in_products.htm
Gentian Violet contains mercury so I would strongly reccomend against using this for Thrush in babies
Here is a link from the government of canada