There are security implications by setting the register_globals=Yes. This article talks about why the register_globals are off by default from Ver 4.2.
Assuming that you are on verion 3, I would imagined that eZ publish 3 will work with the register_globals set to No. This was mentioned in the interview (22-Nov-02) with Bård Farstad
eZ publish 3 was designed to be used with register_globals off. If you have some problems with it I believe you will find the problem to be with the PHP version you are using, either upgrade or downgrade to see if it helps.