I have done this many times. No problems whatsoever. E-6 film is very safe for C-41 chemicals.

When putting C-41 film in E-6 chemicals, however, I believe Kodak recommends that no more than 5% of the total film volume through the chemicals be C-41 film. This means that mixing C-41 and E-6 films in a hand tank with the E-6 process is not recommended (unless you have a 20 roll tank or larger, of course).