If he took the same amount of time to run through the end zone as he did for this momentary kneel, would you flag?
Again, I do not have any issue with what the player in the original situation did- I commend him for kneeling and giving thanks. But why does he need to do it in the end zone, if not to draw attention to his action, and therefore to himself?
Without additional context though, I find it hard to fault the official who threw this flag in the original situation for his action, nor would I find fault with the official if he did not. Similarly, it would be hard for me to fault an official who flagged a person for running through the end zone, or to fault him if he didn't.
Without seeing a specific example of the type you mention, it is hard to say for sure. Each act should be judged individually, in the context of the game. I would never say that I would always flag that action, but I would also never say never either. Even a chest bump, in certain situations, could be viewed as excesive.
Based on your description, I would probably not flag the player for running through the end zone, but there is a lot of information that is missing. Was he running through the end zone toward his sideline, or his teammates, or perhaps toward an official to give him the ball?
Was he waving his arms or doing anything else to draw attention to himself? Was he running toward the other team, or their bench, or away from everyone toward an open area?
If in my judgment, it was any of the first part, probably not. If he was doing things in the second part, then I would at least consider it.
There are few absolutes in these situations, that's why we are asked to apply our judgment. It is assumed that with experience, the official's judgment improves. (and why in most cases, the most experienced officials work the bigger games). If you take judgment out of the equation, by using "always" and "never" than anyone could work those games.
It is certainly possible that throwing the flag may have been an overreaction or hypertechnical application of the rules. But it is also possible that by throwing that flag, it prevented an escalation of oneupsmanship.
If, as was stated earlier, this was early in the game, perhaps it was a good idea to establish boundaries. Taking the religious aspect out of it, flagging this act for taking place in the end zone, hopefully prevents other acts from occurring in the end zone.
If it occurs later in the game, had you previously warned the player not to do these kinds of things? Had there been other acts leading up to this?
We just don't know from the information available, but all of those issues could have an impact on whether or not I throw the flag in this particular situation.