The questions and answers should probably be made invisible or otherwise made low-visibility in search results etc. by some mechanism.
However this is done, though, it should not result in related reputation being revoked.
People who contributed to the site through questions and answers that were valuable at the time should not be penalized for an action completely disconnected from their efforts (the related web service being discontinued).
Retroactively deleting reputation, the way it looks like things are currently being done, could alienate users in general, and it may even make users more reluctant to post on web services that are newer or somehow in question.
Holding to the promise not to devalue any of user's past work might require a new kind of mechanism, where questions are put into a kind of "archived" status with no future deletion (at least of the rep generated by them).
Thanks to AlEverett for pointing out that reputation is not revoked in some cases. These cases are either
- score of >= 3 and visible for >= 60 days, or
- score of >= 3 or visible for >= 60 days
(The relevant MetaStackOverflow post on answer deletion says "and", but the relevent StackOverflow blog entry introducing the exception is unclear.)
If it is "or", then good questions and answers on topics that were once useful should mostly be covered by the "visible for >= 60 days criterion. Not all will be, though.
If it is "and", then the problem remains a big one. There are plenty of useful questions and answers that happen not to get up to a score of 3. If that were a valid criterion, then instead of being applied just for out-of-date topics, it would also be applied to questions that are simply old...but it is not. I don't see any reason not preserve reputation related to all questions and answers deemed worthy of being on the site while the topic was current. If some people think there should be a different standard, though, and want to base it on votes, it should be a lower barrier, such as having a vote score of >=1, or just having no downvotes.