How to make The Tower less of a pain in Carcassonne
We rarely play with either the Tower or the Dragon, mostly because neither my wife or I like having to worry about 'randomly' losing our Meeple like that. and of course the fact that to stop the tower, you have to sacrifice another piece.  

But your question got me thinking, so my idea is to add extra Meeple to each player.  I have two whole sets of Meeple, but you could add them in depending on the number of people playing.  

There are 18 tiles with tower places so if playing a 2 person game, add 6-7 extra Meeple, 6 person game 2-3.  The closer you want it to be toward game design the fewer extra Meeple you add in.

2 players = 6-7 extra Meeple
3 players = 5-6
4 players = 4-5
5 players = 3-4
6 players = 2-3