Basically, the meaning could also be masculine, but it's really hard to find a male form. I guess there are some male secretaries but sekretarz here would sound really strange (it refers rather to somebody like Sektretarz Generalny ONZ). I'd rather use a different word like księgowy (accountant).
sekretarz is a bit different than sekretarka, but why would you replace it with "księgowy" , that is weird. these are two very different jobs. I think depending on the job description "asystent", or "pracownik sekretariatu", may be used, if you think "sekretarz" is too esteemed name for the position.
You're right. I overdid a bit with that księgowy :) To my understanding (probably with a bit of ignorance), it was something like accounting assistant or accountant and could be used to describe a similar position in a firm. But perhaps they're much more different.
But consider that księgowy is not so much more different semantically from secretary than sekretarz because, as you mentioned, sekretarz usually has a somewhat different meaning. I just couldn't find a good word for it. The ones you proposed are much better. Thanks.