Yea, that's more or less how I ran it when the PC's were trying to clear out the Cog, a large industrial spire/train from Lure of the Expanse. The overall opposed Command check was boosted by the various PC's contributions of Tactica Imp to plan, Stealth to scout, Tech use to hack doors and find functioning cameras.
Later it became Medicae to keep the casualties down, stealth again to snipe hard targets in the larger bays, tech use to turn some of the heavy machinery against the enemy, and awareness to keep a feel for the overall battles to know where they need reinforcements or where the enemy seemed weak.
For the third act when the overall battle was more or less a foregone conclusion they found that the whispered were setting up a small nuke for the ole "If we can't have it nobody can." They had to go take care of that as the "boss fight" while their forces made the final push around them.
That last bit is another reason why the RT's might not choose to bring lots of soldiers and helpers with them. If you want something done right, do it yourself. The PC's are invariably more skilled and able than their helpers and hirelings.
Sure you could send a couple of platoons of house troopers in to clear out the building, and you'll be able to successfully clear it out, but there might not be much building left once they're done and they might miss the hidden safe containing information on who's the mole in their organization, or set off a trap on the safe destroying the contents, or maybe they'll fail to talk their way through a standoff and wind up killing some NPC's that could be turned to your side.
Edited by Spatulaodoom