I believe using a pot and water you can at least use a variety of fruit for dyes.You could also invest into a cheap food processor if you really wanted,but that's definitely not necessary.
Soy paint generally is considered safe,however an even better choice if you want to have the option of knowing every single ingredient in the paint you use the link below is an excellent choice(does contain clay but as of late it's seeming more like that's only an issue in litter form or as a powder and not when mixed into foods,paints,etc of high quality)
Old Fashioned Milk Paint is a natural chemically safe, environmentally friendly paint