Tried it... got derailed due to the fact that the group decided we wanted to play something other than Shadowrun, but it had some great potential.
The biggest hurdle I was face in doing this kind of campaign is how are you going to handle gear requisition and to a lesser extent payment. As company men their lifestyle being covered is expected but what limitations do you put on what gear they can have. Do you pay them for runs and then require them to buy their own gear for extra deniability, etc.
That's the easy part, really. The first question is, of course, where on the food chain you want them in terms of "eliteness". Do you want them as the equivalent of a Corpsec High Threat Response team? A standard "Military Equivalent" unit? A squad of something ultra-elite like S-K Prime or Aries Firewatch? Some super-duper-special mega-soldier project?
Once you figure that out, give them appropriately loosened "Availability" restrictions, with an extra budget for gear above and beyond their 400 BP. The catch? They can't spend any of their own BP on gear and they can't take the Restricted Gear quality, plus they get saddled with Negative Qualities to balance out the bonus-cash. These, of course, give no actual BP and wouldn't count towards their Negative Quality total.
Since this sounds most like something in the HRT-to-Military-Equivalent range, I'd recommend going with an Availability of 20 and 150,000¥ for starting equipment. The balance is SINner, Day Job (40 hr version, enough to cover a Middle lifestyle), Records On File, and Bad Rep (applied to shadowy dealings only, not the corporate side of things) as "freebies" as well. Encourage them to also take Corporate-Owned as a Negative Lifestyle Quality.
Give them their "payment" for runs in the form of a gear budget.
Their starting gear will, invariably, include things like Heavy Military Armor with chameleon coat mods, etc. Don't worry about it... they
should have stuff like this, given their positions. Once they drop into the Shadows, assuming they're smart enough to get all this starting gear out with them, their need to keep a low profile will severely restrict its usefulness.