This is a very common mistake, since the name “Johns” is not one that is encountered outside the name of JHU.They do make lots of jokes about it in the promotional materials, tour, and so forth that I would have hoped had made an impression earlier in your pre-application research.
Perhaps you were misled by this story from April 1, 2010. 
http://www.washingtonpost.com/wp-dyn/content/article/2010/04/01/AR2010040102179.html
I hope they will not hold it against you.