These days the mobo's are protected from current overdraw. In the old days if the fan was to high in current, the fan headers would blow out. These days modern mobos from names like Abit and Asus it's highly unlikely the mobo fan header will blow out, what will happen is the mobo will not boot if the fan is not within specs for the fan header
But if you have a fan with a very high power draw, just use a molex adapter, and just strip all but the yellow tach wire from the 3 pin fan header, and just plug the tach wire 3 pin plug in the mobo fan header, and the other 2 wires to a molex adapter, this way you can still monitor rpm's if you so choose.