It would have been wiser to let the kneeling controversy die down on its own, but one can see where the league is coming from.
Picture the Google homepage. Now imagine that a small team of engineers responsible for updating its look each day attached, without clearance from their bosses, a small emblem of an American flag with a red slash drawn through it, and explained to anyone who asked that this was a political protest they planned to continue indefinitely.
Would Google tolerate that? I doubt it. Should it tolerate that? Certainly not. Millions of users, maybe tens of millions, would presumably switch to another homepage. The stunt would cost Google significant revenue and unwelcome publicity. Knowing this, it would order the engineers responsible to knock it off, and if they failed to do so, remove them from their jobs.