Here's how we handle it. If you have to push a guy down, you lose another draft pick later in the draft also.
A-Rod and Pujols were both drafted in the first round, and you want to keep both. A-Rod would cost you your first round pick, and Pujols would cost your second. Since Pujols was "pushed down" from round 1 to round 2, you would also lose a 10th round pick as well.
This year, I had to push down three guys as a result of trades, so I ended up losing picks 1,2,3,4,9,10 and 11 just to keep four players.