Hmm. Yes, I think you did something wrong. I was in a similar situation. I had a database that had hundreds of tables replicated. The snapshot was 9 GB. I then needed to add one more table. I obviously did not want the whole database to be snapshotted again. I just added the table to the subscription and generated a snapshot. The snapshot agent ran and created a snapshot of only the new table and sent that over. FYI, this was on SQL 2000.
Did you stop replication before adding the additional table? If you did that, that might cause all the tables to be included in a new snapshot.
The link you gave specifically states a new snapshot of the entire publication will NOT be created: "After adding an article to a publication, you must create a new snapshot for the publication (and all partitions if it is a merge publication with parameterized filters). The Distribution Agent or Merge Agent then copies the schema and data for the new article to the Subscriber (it does not reinitialize the entire publication)."
In my case, I was also only using transactional replication. You never mentioned what kind of replication you were using, but you did mention the merge agent, so perhaps you are using merge replication?
In any event, you stated the whole snapshot was being sent, so I don't think there's anything we can do to stop that now. Hopefully it is completed and things are running smoothly again.
What I did in my case, was to set up a test using a second replication publication that was similar to my live publication, but with fewer tables and data, then tested adding a table to that publication and see what happened. Perhaps next time you can devise a similar test scenario and see what happens.