The Saiyans are already evil, wheter Freeza is commanding them or not, so much so Vegeta wanted to be the next ruler of the Universe and I doubt he would do it in a fair way.
The root of evil is just a figurative way of referring to the biggest evil. Piccolo Daimao also muttered before dying that the root of evil mustn't be severed when he left behind his offspring, but it's not like either of them are the origin of evil