Doesn't make a difference to me. IMO, part of the challenge of being a GM is dealing with injuries, whether it's by claiming FAs/waivers, or digging into your farm system. On the other hand, injuries seem a bit too far out of hand, so there's that argument.
Are injuries even something that can be changed after we started though?
As for the game automatically putting players in the wrong position. I think it's because it's designed to replace the position with whoever is the best rated that isn't currently on the starting roster. When I had over half my starting forwards injured, it stuck my scratched dmen in forward spots rather than call up forwards.