PoE Design for Camera Interface Isolation Question
The MDI Pairs will be going directly to the ethernet PHY on the
  camera. Does it not send ground A to ground B directly? Ground A and
  ground B be the same because of the MDI pairs going to the PHY on the
  camera? If this is the case, would it not defeat the purpose of the
  isolation transformer?


The Ethernet magnetics can provide isolation, depending on the transformer you buy, I've seen some go up to 4.5kV. The MDI pairs are isolated from the cable at the ethernet transformer. 

However, if the ground from the MDI pairs was connected to the same ground as the POE circuit before the isolation transformer, it would provide a direct pathway to the data lines.

If you isolate the data pair ground from the Powered Device (PD) ground and isolate the PD controller with the isolated DC to DC converter (as discussed in your post) then you should achieve the isolation you want. (in short, keep the PD controller on its own separate ground that is shared with the cable). 


  Our camera is mounted against a metal chassis that the user will touch
  when connecting power. What effects will this have on the user and the
  camera since the user would have a different ground than ground B. We
  want to make sure the camera does not get damaged.  


You can use isolation or a plastic box. Tying the ground to the chassis isn't going to be a good idea, ESD needs a return pathway and sending it back thorugh the POE power lines is not good either (the ESD will then be on the power lines of the PD and PSE). This is why isolation is required. 


  Terminal side (DTE) - The IEEE 802.3af standard calls for 1500 VAC
  galvanic isolation between the link, the chassis ground and the DTE
  circuits. Since in many systems the power supply’s return is tied to
  the chassis ground, for enhanced EMI reduction, a conflict may occur.
  The required Isolation may be achieved using the following two
  methods: 
   - Power that is fed over Ethernet is isolated from DTE circuits by an isolated DC/DC converter that withstands 1500 VRMS. 
   - The  terminal  is  housed  in  a  non-conductive  casing,  with  no  external  connections  other  than  the  RJ-45  data  and  power 
  connector,  resulting  in  the  internal  power  supply  input-output 
  no  longer  needing to be electrically isolated.


Source: https://portal.chippc.com/support/downloads/files/PoE_and_IEEE802_3af.pdf