I know that your question was posted a while ago, but I found a better solution. Do the following:
1) Open "Sound Settings"
2) Find and click on "Sound Control Panel"
3) In the popup window click on the "Sounds" tab at the top
4) Under "Program Events" scroll down and click on Default Beep
5) Select the dropdown menu under "Sounds at the bottom of the window. Scroll to the top and select (None).
6) Click Apply
The sound no longer occurs after a search in e-Sword. This may disable the sound for other things as well, so be aware of that. But at least now you can search AND use the enter key without that annoying ding.