Removing Assassin in 3 players game
I think this would actually be less balanced. 

Assassin
From the perspective of the choosing player, the main strength of the Assassin is rarely the actual assassination. The Assassin's main strength is actually that since he plays first, he is able to avoid attacks by the Thief and Magician. (Occassionally the Assassin's player will benefit directly by eliminating the Magician or Warlord)

The player who generally benefits most from an assassination is the non-involved player, since (unless he took Warlord) is the only one who can take two actions towards city improvement.

Thief 
The thief in a 3-player game still has a lot of things that can go wrong.


He could be killed by the Assassin prior to being able to steal. 
If one opponent has coins and the other does not, he has a 50% chance to choose the wrong player and get no money.
If he only sees roles late in the rotation, (ex: Merchant and Architect), there is a good chance the target will also have an earlier role and have spent the money already.


Probable Effects of Removing Assassin and Thief
This would be extremely unbalanced.  Can you imagine a game where the Magician goes first every round?