Maybe if they get like -1 for every skill if their injured for 1 week, -2 for every skill if their injured for 2 weeks,(etc).
In case you don't understand what i mean if player A is injured for 3 weeks and has tremendous JS it will be reduced to prominent. That way if a manger's star player gets injured they still have the choice to play him.
Just adding another suggestion: Instead of saying Player A is injured for 2 weeks which can range from 14-21 days, just say how many days he will be out. It will cause less frustration and confusion.