Well, I have worked in Greek Life before, but I never heard of a situation like this one.
I'm not sure how the campus classified them in the first place as both a fraternity and a sorority (independently) if they did not have any female members. You mentioned that they do not consider themselves to be a co-ed fraternity, but how can they not if they are planning to accept women into their chapter?
I think this organization really needs to rethink its structure before moving forward. Hopefully they have a strong female faculty or staff person advising them, along with any male advisor they might have. As of now, they are probably planning to have the women go through a process that was designed with men in mind, and this is not necessarily a good thing (nor is it good to have a male in charge of a female pledge group, because depending on the person in charge, he may abuse his authority in various ways). As a female, I would feel very uncomfortable (more like CREEPED THE HECK OUT) by having males in charge of my membership process.