That would work.
The thing about player's leaving there team during the season has been a concern for me also. It happens too often.
I have a twofold thought on that.
1) Have a vacation mode, which shows a player is going to return, he is just away. This allows the AI to make adjustments to the depth chart for injuries, and update the gameplan... but do nothing with personnel unless required due to injuries. This would need a time frame, with a max of 3 to 4 real life weeks.
2) If a player doesn't log in to his team for more than a real life week, and is not in vacation mode, he should be removed from the team, his 5 credits lost. This allows another player to come in and take over. Moreover, it allows the AI to actually start to run the team. A player taking over a vacated team would get to play the rest of the season for free. The 5 credits is already paid, and it gives some reason for a player to take over a vacated team in the middle of a season.