Personally, i would have asked for the station manager at that point.....no way i would have taken BS like that. My dep airport is philly and i usually have good experiences with us employees (way better then pit).
Write a letter....and call. If someone is going to work in customer service...they shouldnt have an attitude like that.
Also, Im pretty sure it is possible to credit different segments to different FF acct numbers. It is probably best to do it with the gate agent.