I agree with River in that while poly is a lovestyle it is also a discourse. Words are important, and they shape reality.
I think that primary and secondary imply hierarchy. It may be the connotations of the words themselves or it may be a cultural thing, whatever. It's there, if not for all, for many. That's why I don't think it's wise to use those words unless one wants to convey the message of the relationships being more and less important. Even if that's not the meaning the person using the words personally attaches to the words that is the meaning they convey to many.
I think it is problematic that many people in non-hierarchical relationships use primary and secondary labels. This is particularly when thinking about polyamory in relation to mainstream monogamous culture. I am sure that to many monogamists the terms primary and secondary refer to hierarchy (as they seem to do for many poly people, while not for many others, based on this discussion). Therefore, hearing those terms to be commonly used by many poly people, even in non-hierarchical relationships, gives the picture that poly relationships are most often hierarchical. Of course, even a poly structure where there actually is a more and a less important relationship still challenges the mainstream monogamous culture. But using hierarchical language in polyamorous relationships, even in ones that are equally important, enforces the so common belief that people really can't love equally, i.e. one must love one more than the other or polyamory involves no Real Love at all.
(Disclaimer: please note I'm not saying you must not use the terms primary/secondary, only voicing my opinion.)