I understand that point, but I must disagree on this call. I was watching the game live and was shocked when the whistle blew at that moment (so was the broadcast crew). Philadelphia was literally just about to shoot.
The ref should have let them get the shot off. It would have been only a couple seconds over the allotted stoppage time; which, after all, is not a hard-and-fast number to begin with. Referees let plays develop at the end of stoppage time in multiple matches across every league every weekend in the interest of sportsmanship.
If they shoot and miss and it's a goal kick, blow the whistle. If they shoot and miss and there's a rebound and Atlanta clears their lines, blow the whistle.
If there's a rebound and Philadelphia immediately gains possession, judgment call. If they pass for an immediate shot again, let play continue for a few seconds. If they back pass and recycle, blow the whistle.