Below is the Apple license agreement for the Mac App store, accessed on 24 January 2012.
According to a layman's reading of the text (I am not and do not pretend to be a lawyer), what you describe should be both possible and allowed under the terms of the license.
You or your IT staff would log in to the Macs, authenticate to the Mac App Store with your company Apple ID, install the App(s), then sign out of the Mac App Store. Your employees could then log in with their personal accounts and install any Apps they may have purchased, although according to the text in section i, they shouldn't do company work with their personal apps.
I hope this is helpful.
MAC APP STORE PRODUCT USAGE RULES
Except as otherwise set forth herein,
(i) If you are an individual acting in your personal capacity, you may
download and use an application from the Mac App Store (“Mac App Store
Product”) for personal, non-commercial use on any Apple-branded
products running Mac OS X (“Mac Computer”) that you own or control.
(ii) If you are a commercial enterprise or educational institution,
you may download a Mac App Store Product for use by either (a) a
single individual on each of the Mac Computer(s) used by that
individual that you own or control or (b) multiple individuals on a
single shared Mac Computer that you own or control. For example, a
single employee may use a Mac App Store Product on both the employee’s
desktop Mac Computer and laptop Mac Computer, or multiple students may
serially use a Mac App Store Product on a single Mac Computer located
at a resource center or library. For the sake of clarity, each Mac
Computer used serially by multiple users requires a separate license.
(iii) Use may require sign-in with the Apple ID used to download the
Mac App Store Product from the Mac App Store. Mac App Store Products
can be updated through the Mac App Store only.