Yes, obsolete comments should be removed. Always. We even have a flag to clear out 'obsolete' comments that may have been missed.
Comments were included with every post for a purpose — to ask for clarifications or otherwise help improve the post. Comments are there to help facilitate the wiki-style editing in Stack Exchange that helps assure every top-voted answer contains the most complete, accurate, and current information available for that answer. Questions are improved in a similar manner.
But once comments serve that purpose, they should be removed.
We don't want to create a situation where, after every answer, the user has to pour through a series of addendums to see if the answer is actually complete… or is it the start of a meandering conversation where we swerve into the correct information at the bottom of page 18. That was one of the failures of threaded discussion forums which prompted the creation of Stack Exchange.
Once comments have served their purpose, they should be removed; otherwise, it's not clear whether the vetted answer is actually the complete answer or not.