Yep, it's true. "MySQL Toolkit" technically infringes on MySQL's trademark. I haven't been given a mandate or cease-and-desist order or anything, but as Marten Mickos (MySQL's CEO) told me, anything that starts with the word "MySQL" sounds like it comes from the company, and this project doesn't come from MySQL.
Suggestions are welcome. I'm totally uninspired. "Toolkit" was the best I could do when I named the project to begin with.