Isso é abordado no script do filme. Em resumo, a onda de choque causada pelas explosões nucleares e secundárias dos vasos de Chitauri era visível da superfície. O Capitão América queria fechar o portal antes que ele chegasse.
EXT. SPACE: We then see Tony's horror. AN ARMADA. The black sky is filled with what must be ninety ships in a vague cluster. Most of them hang still in the air. Some move swimmingly about. IRON MAN lets go of the missile. It whistles off into the blackness as IRON MAN IDLY falls back down the portal's opening. The missile reaches the MAIN SHIP. The MAIN SHIP IMPLODES, causing the entire ARMADA to burst into a supernova, creating a spectacular heavenly display.
... [shortly afterwards]
EXT. MANHATTAN DAY: Thor and Cap see the supernova coming towards them. Thor nods to Cap.
CAPTAIN AMERICA: (to BLACK WIDOW) Close it.