I would be concerned, especially since you make it sound like this just started happening. I drive a couple accords (one auto, one standard) and both have over 210k miles and neither make any weird noises when shifting between reverse and 1st. There are another 3 accords in my immediate family and none have this issue. I've replaced the driver side CV shaft in my accord and the rebuilt unit started clunking after about 1000 miles. It simply was a poorly rebuilt unit and I exchanged it for a another one under warranty and have had that one on for probably 20k miles with no issues. If I were you I would get a 2nd opinion or go back and complain if the noise wasn't present before this work was done.