I opened a ticket looking for a solution to this after not finding one in the wiki or the forums here. In response I was directed to this thread, and this bug:
Bug 23275 - Yahoo search engine hardcoded . This whole thing really upsets me too, but at least they were responsive about it via trouble tickets and say they are working on a fix, ASAP I presume. I have a 5.0.1 install and was not able to remove yahoo search, even after removing the yahoo local zimlet.