Mike,

Disconect the field wire from the regulator and it will turn the alternator off so it cannot damage anything. I am making a huge assumption here that they have the large regulator, which at this point may have been fried. The guts to them are also available from Elreg.

You might check these folks for your alternator and regualtor as well.

http://dixie-electric.com/catalog/9801-50DN-003.pdf