I had the same problem, and I took my computer in to the shop and got the card replaced under warranty at no cost.
I am unfamiliar with the electronics of the card, but I would imagine that if there are really only those two wires then taking out the fan wouldn't hurt anything. reconnecting the wires would only be required if that same piece of circuit were bringing power to other components on the card (which is probable). in which case the card might have a problem with too much current resulting from the removal of a branch from the circuit if it's connected in parallel (though all other components would still function). or if the circuit is connected in series components will not work at all unless you reconnect the wires, in which case there might be problems due to a too high voltage resulting from the removal of a rather large resistor (the fan).
I have no idea what kind of effect this might have if any, and don't know enough about EE to give a recommendation.
[This message has been edited by elzinat (edited 04-19-2001).]