It's been said that there is a DEA because Hoover knew drug enforcement would corrupt his agents.
I think the only reason the FBI wouldn't welcome them with open arms (after all they worked so well together at Waco) is the inherent snobbery of the FBI as being elite so that they once had to be either lawyers or accountants to be a special agent....whereas any old brutal cop with his own jack-boots can get into the ATF.