While randomly making a choice might be the fairest way, it is not the correct way to proceed. Each option yields an impact on the game, so the decision must be chosen.
People against scientific great leaders might argue that a free wonder in 3000BC is overpowering and unbalanced. It is based on luck, and as we all know, luck is a huge factor in Civilization III. The spearman defeating the tank is a classic example. That outcome is based on a huge stroke of luck, and as such, we can't rule that outcome out of the game. In addition, the team with the wonder will find themselves in a particular situation - they will have to use their diplomatic skills to the most effect; most teams probably want that wonder, and will do anything to get it. Thus we have a situation that requires cunning, smarts, and luck to get out alive.
Therefore, it is my decision that scientific great leaders are to be on.