The LBS advice isnt bad, but there are better ways to get pads bedded in which should reduce the noise.
Going that it's a new bike, the discs and pads should be clean with no contamination from oil, the brakes need to be bedded in, you can google how to do this, or there is a guide here
http://www.bikeradar.com/gear/articl...ke-pads-31337/
Some discs will always make a noise, some won't do they stop you? as thats more important than a little noise.