1) it's only a fucking copy, the original is still back at the house, swarming with Makarov's men or the Russian Military
2) why didn't they just rip the fucking hard drive out of the computer or take the entire thing, it's not like this was supposed to look like didn't want the their presence noticed.
3) if Shepard wanted the data destroyed, why not just bomb the fucking building, hit it with napalm. Why did he order a copy made and brought to him?
4) why did he kill these loyal soldiers who suspected nothing of him, hell there wasn't even a hint of this betrayal? Just invite them onto the helicopter and discretely at a later date destroy the drive, if they ask them anything tell them the info was useless and send them on another mission to catch Makarov.
5) if he had to kill them, why kill them WITH HIS OWN GUN! Smart thing to do would be to just leave them there for the militia to kill, or order them killed from range... make it look like friendly fire. Less witnesses.
6) I mean the US Army/Air-force pilot "say, what's that burning smell and OH MY GOD, Shepard MURDERED those two British special forces personnel! Burning their bodies, didn't even try to arrest them! Not self defence at all"
This is the problem with conspiracy theories based around killing off "loose ends" every one you kill you have to kill 5 more for those who witnessed said killings or who committed the killings themselves. How can Shadow Company keep this secret but not Task Force 141?!?!