That general plan sounds right to me. I would recommend setting a player as starter, backup, and reserve for the game where you want him to play all 48 minutes (not sure if you meant this or not). This will work well most of the time.
One thing that can cause an issue is if you are blowing out the other team, and are winning by 20+ points in the 4th quarter. In this scenario, your coach will always try to take every starter out of the game, including your trainee. The best way to avoid this is to have no extra players sitting around; if there is no one available, then your trainee will stay in the game by default. If you are forcing 48 minutes at one position, using just 9 players for the game helps avoid any problems caused by a huge lead.
I wouldn't be concerned about injuries, and the game shape effect is the same as if the player played 48 minutes for the week in any other way.
A player will generally play worse if you play them for a full 48 minutes, due to stamina issues. How much of a performance hit varies from player to player, but stamina is definately a factor.