Oh come on, unless you avoided touching ANYTHING the entire day you touched something every other person did. You aren't getting any other disease from the finger scanner than you would from using a door handle, the grab handles on the rides, any plate, drink or other item handed to you from any other human, etc. If you were really that worried about disease a $1 bottle of Purell would solve that one time finger scanner touch.
they have been trialing RFID for a long time and have many of the machines already installed. If they are using ipod touches to scan tickets I can assure you it is because there is an issue with something or as a stop gap measure while they flip the switch on the magicbands since they wouldn't be able to do the biometric scan on an ipod touch so there is nothing to prevent you from using someone else's ticket. Either that or they are scanning tickets with an ipod touch for people who have tickets without RFID and will still make them scan their finger and go through the turnstile as normal
I just came back from a trip down to Florida. The reason why they still use the old turnstiles and the iPod touch scanner is to provide support for people with the old tickets without the RFID chip. People who purchased their tickets in advance through external companies, are still getting the old tickets that do not have the RFID chip in it (i'm guessing just leftover supply of old tickets). Everyone else who purchases their tickets at the park are getting the new tickets with the RFID chips. They only have a few old turnstiles and iPod touch people at the entrances, but there are predominately RFID turnstiles.