Probably worried about mass hysteria. And the inevitable bitching over the fact that it's the US that decides how human relations go with alien races. To be honest I'd probably keep it quiet, too.
Like you, I'd keep it mostly the same. SGC is actualy a fairly competant organisation. I'd probably try and recruit more personel into it, and boost the team numbers up from 4 to 8, to increase their chances of survival. Perhaps work on some sort of ground vehicle that can fit through the gate (couple of Humvees?) to allow teams to cover ground faster. Other than that, not much I can think of.
"You've all been selected for this mission because you each have a special skill. Professor Hawking, John Leslie, Phil Neville, the Wu-Tang Clan, Usher, the Sugar Puffs Monster and Daniel Day-Lewis! Welcome to Operation MindFuck!"