I'm trying to recall a short story from the late 1940s or 1950s about ex-soldiers being recruited by a shadowy agency who then end up fighting in a far-future conflict. The chief recruiter employs a human woman to act as office staff and she stumbles on the truth.
That's almost certainly "Recruiting Station" by A. E. van Vogt, first published in ASF in March 1942. It's a point-for-point match with your description. Norma is the secretary who discovers what's really behind the recruiting station she works at -- and she ends up as a double (or maybe triple) agent in an intergalactic/time travel war.
It can be found in a number of anthologies and collections: http://www.isfdb.org/cgi-bin/title.cgi?68329
Incidentally, if you enjoyed that story, Michael Swanwick "Legions in Time" wrote a sort-of sequel, sort-of other view which is excellent.