I'm not sure the AI uses caravans to build wonders. I think they just get shields from time to time for whatever they are producing. So, you could just not use caravans to build wonders. Interestingly, while you can change the Game.txt file to stop human players from choosing certain options in many menus, the caravan choices are found in Labels.txt instead.
The map size doesn't change many rules in and of itself. I think some costs/benefits are scaled (the caravan delivery bonus comes to mind). Some changes might be linked to the map size specifically chosen. I think I remember a 100x100 map having the normal 'riot factor' (unhappiness based on number of cities owned), when a 'large' map should have a different calculation.
TOTPP 0.18 added support for a "TradeWonderMultiplier" setting in @ COSMIC2. This is the percent of its normal value that a caravan will contribute to a wonder (default is 100). So while it's true that the option of doing this will always appear in the list presented to the human player, and you can't technically prevent them from choosing it, you could set this to 0 percent and then change the value in Labels.txt accordingly, to let the human player know that choosing that option simply means their caravan will be lost and contribute nothing ("Disband caravan with no effect").
