I do not know enough about K theory myself to be comfortable making the call. Please discuss. If we reach a consensus, I (or Qiaochu) will implement and document the change on the tag-merger thread.
One of the issues is that there is not a lot of traffic in these tags (I imagine). In general I think having more tags is best, this may or may not be one of them. One possible reason for the plain K-theory tag is that there is an arxiv tag that is more applicably described by K-theory than the other two. In the early days, I think people able to make tags were trying to mimic the MO policy of having one for each arxiv area.
I think that there are conceivable questions about K-theory that it might be misleading to tag as just algebraic or topological K-theory. But I strongly doubt those questions would be asked here.
I personally use tags to learn about the views of the asker, and what type of people they want to see the question.
Some of the above are just general comments.
Maybe (algebraic-K-theory), (topological-K-theory) and (operator-K-theory)?
But probably, we should just wait.