The way the shields deployed in TWoK may offer a clue to this question of how the fired photon got through Grissom's shields. The graphic does not show the shields simply "turn on." They take at least a full second, as all of the lights encircle the outline of both Enterprise and Reliant. And movie time is very hard to gage or go by. Kruge tells Kirk he's got 2 minutes to surrender in the story, but onscreen, Kirk's takes a good deal more than 2 minutes, farting around with Destruct Codes and beating feet through the corridors, until he gets to the transporter. But that's just an example. It's very hard to tell in movies what amount of time is truly being represented.
So ... between that and the Shield Activation graphic, the BoP had ample time to sneak in a photon, before the Window of Opportunity closed, completely. Besides which, as "by the book" as J.T. Esteban was, his crew was probably no less so. If there was a checklist that the handbook recommended before employing the shields, it's a good bet that the appropriate officer used it. Who knows when the last time he had to, anyway? It probably took him a moment to remember where the switch for it even was, in fact ...