In fact, Alexander Pierce received the news five minutes after Sitwell was kidnapped by Captain America and the others.
That bald brother wasn't acting alone; he had four security agents with him. Although he had sent them away for a while when he took Sam's call, when they returned, they discovered, Holy crap, their boss was gone! What was going on? Looking at their boss's hairstyle, he definitely hadn't gone to get his hair done. So they reported it to their superiors.
Pierce had actually valued this subordinate, who had performed increasingly well over this period. So after Sitwell was possibly kidnapped, his first thought wasn't that the man had betrayed him. Instead, he believed Sitwell would remain steadfast, die defending the organization's secrets, and never cling to life in disgrace.
But after he finally connected to Sitwell's phone signal and located his position, he discovered, What the fuck? He's already leading people straight toward S.H.I.E.L.D.!
Traitor! Shame! Pierce, whose feelings had been deceived, was utterly furious. Three generations of service, trained from childhood, promoted for over a decade, an oath on paper—all burned to ashes, burned to ashes!
After suffering betrayal, Pierce finally understood Nick Fury's feelings a little. But he was still a formidable figure. After flying into a rage, he immediately regained his composure. Sitwell had defected, which meant Captain America and the others surely already knew Project Insight's true purpose and were heading here with people. Under normal circumstances, that would indeed have been a headache, but not today!
You wasted too much time. After being attacked by missiles in New Jersey, you should have come straight here, but you waited an entire day. A day was enough to change many things. For example, there were only sixteen hours left until Project Insight officially went online.