Wordfence shouldn't be a factor here. We recently did this for a site I manage. The deciding factor was that MyISAM locks the whole comment table if someone writes a comment to your site. InnoDB does not. I'm not a DBA, so I'm sure someone should come along with a better explanation, but our site is very high traffic, especially around the holidays. Switching to InnoDB was one of the things that helped us reduce load. I highly recommend it.
tim
