This is an old question of mine, but then again at least I found a way to resolve it.
I was able to remove the publications is by creating a new publication with the same name, then delete the publication again. This time the publication will no longer appear in the Replication Monitor. I did not remember if the publication has to be the same type as the obsoleted one, but it works.
UPDATE: Okay, the publication type and database name is important, otherwise the newly created publication will be considered as a different publication. Kinda obvious, but now I'm sure of it.