Delete time zone entry in Calendar's list
Terminal:

defaults delete com.apple.iCal 'RecentlyUsedTimeZones'


removes all recently used time zones.
(Close Calendar app beforehand.)

I'm pretty sure (but please, someone prove me wrong) the defaults command can not delete single values within keys.

If you have Xcode installed, you can open the Calendar/iCal preferences file located under ~/Library/Preferences/com.apple.iCal.plist

You then search for the RecentlyUsedTimeZones key and manually delete the unwanted items within the key by clicking the (-) icon next to the item number.