There is an easy, simple way to deal with the issue: sell your national player, purchase player of the same strength that is not an NT player, and stash the rest of the money. Or never buy a player with a flag.
I can tell you right now that withdrawing a player from the NT will never be an option for gameplay reasons.
That is ridiculous. Why would want to offer our players up for the sake of the game? It sounds selfish, but fair. In real life, you get the say if a player may or may not play in the NT.
So you are saying, that people should treat a player being in the NT a bad thing. Therefor resell them and replace them with worse players that are not in the NT.
And once they get selected for the NT, i should replace them again. Why should the NT result in such a troublesome routine?
By far the easiest way to solve this, is just remove injury from NT games. Not your way of trading players. Sure, it's challenging, but what's the point?
On top of that i could easily find a way to abuse this rule, in order to win the first league, as an NT coach. Not that i'm an NT coach, but you might see people invite a top-notch player from a competitive team in order to try and injure him via NT matches.
Once a player is branded an NT player, the manager will receive a handicap. An extra chance of an injury, without any advantages/compensation whatsoever.