Honestly I would recommend removing none of the roles as the game is decently balanced for a game with random rolls and you just got bad luck.
From what you have posted it seems you are missing some of the rules for the game. First what you described to have played was not one game but one round of a game that lasts 3 rounds.
It also sounds like you had bad luck in that all 3 saboteurs where present in a 6 player game which is not all that common. I would also question why you would discard path cards just because they have a crystal on them since they can be critical to winning and you will win more then a single gold in most cases.
The last thing that I am wondering about is from the way you worded your question it seemed like everyone knew what role everyone was. If that is the case it would allow the saboteurs to have an advantage and target the miners and all players to have an advantage to discard crystals.
My advice would be to play at least 1 full game of 3 rounds where you will see different team balances for each game. Though to get a true feeling for the balance of the game I would suggest that you play more games so that a bad draw does not influence your opinion of the game.
It should also be noted that the roles in the game can change at any time as there are 2 action cards that cause a player to switch roles which could be good to get rid of an enemy or prevent someone from making a lot that round.
Based on your updates it definitely sounds like you where not playing it optimally
- At the start of the game everyone should be acting like a miner regardless of their role. This is a hidden role game and you don't want to reveal to much information to start. Every game I have played has started with the saboteurs trying to make it look like they are miners before starting to cause damage to the mine. This is especially important in a larger game where there is only 1 saboteur so they don't become targeted and rendered useless early on. Note once you have more games under your sleeve and have a better understanding of the game and the roles then it is more feasible to come out with your role earlier in the game.
- Miners and saboteurs should not be discarding path cards with crystals on them just to prevent the geologist from getting points because every discarded path card could mean the difference between them getting gold or no gold. Note this does not apply to cards that prevent you from reaching your goal.
- You should also remember that in this expansion there are cards that prevent people from getting gold and cards that let you steal gold from others. This means that even if everyone ends up on the same team and wins not everyone will end up getting gold or the same amount in the end.