Is it grammatical? Yes. Does it sound natural? Not really.
The problem isn't the grammar. The problem is that there's no obvious reason to relate "the boys playing football" to "Susan's arrival". Is the game somehow meant to prepare them for her? Is Susan planning to check with the boys to make sure they played their game? It doesn't make sense.
Instead, what I think you want to say is that the boys were finished with their game, and therefore ready to do whatever it is Susan intended to do with them.
The boys had finished playing football before Susan came.
Otherwise, if the boys played football and then Susan came, with no relation between the two, just use the simple past:
The boys played football before Susan came.
Of course we can conceive of some strange scenario in which "the boys had played football" makes sense -- but do you really want to learn about unlikely relationships of events, or how to talk about likely events in a natural way?