Smells like more banishment of what culture puts in the box labeled "religion" to an unnecessary extent. Apparently, because the "secular" pep talks routinely given before a game are not put in the "religion" box, those are okay, even though they are functionally or precisely identical to various "religious" prayers.
There was an insightful comment I ran across in a reading somewhat recently regarding the reality of what "separation of church and state" actually means. Going to have to follow up on the literature there at some point, because it was quite poignant. Basic thrust of it is that this attempt to maintain separation basically just serves to hedge in what we call "religion" and what we don't call religion in a way that expresses strong cultural biases. As a religious minority I notice this a lot, as expressions of my religion would be put in the "secular" box and get a free pass. It's stupid, and inherently unfair.
Two competing thoughts leapt to me when reading the OP;
1) There doesn't appear to be any coercion, so let's not over-react.
2) He's in a position of authority (as a teacher) and therefore in a position of influence.
Balancing off those, I think it's better if he doesn't continue what he's doing given that it's against school policy. I'd be interested to know what you mean by 'secular pep talks' in particular, and how you'd see those as religious, or in either encouraging or discouraging religion. I'd also be interested if you do manage to dig up the literature you have mentioned re: separation of church and state.