If you are going to train Free Throws, then it should make no difference whether you play the scrimmage or not.
I don't think 5th place should get anything. They already get the gaurantee that they won't be relegated. I understand that you don't think it is fair that the 6th place gets a better draft pick, gets income from the relegation game, and if they don't get relegated end up ahead of you. But you didn't have to come fifth, if you would prefer to be 6th, then make sure you come 6th.
I also understand that if you are in the lowest division then 5th place is a bigger disadvantage because 6th place gets extra income, better draft pick and no chance of relegating, but everyone already knows that 5th place doesn't provide a benefit other than not relegating, so it is your responsibility to make sure that you don't finish 5th. This brings more tactics in to the game which is good.
Also, if you are in 5th place, simply train Free Throws or Stamina, there is no harm, you are going to train it sometimes anyway so why not now.