Parallel to less parallel without throttling
If you cannot stop the camera/packetizer from sending 32 bits per clock, then you either must do one of the following:


Implement a huge FIFO in your logic which can store the overflow. If you have 16 bit output and 32 bit input, then the fifo must be large enough to store 50% of the total size of the camera image (as you can send out half the bytes as they come in). If you have only 8 bit output, then the fifo must be large enough to store 75% of the total size of one frame. Note if you do this you must allow time for the fifo to clear before starting the next frame.
Make the output clock faster than the input clock. Needs to be 2x faster in the case of 16 bit output, or 4x faster in the case of 8 bit output.



  Is there a nice way of modifying a state machine to handle these edge cases?


Not really, you just have to specify the behavior you want. There's not a magic statement that will automatically handle it. My suggestion is to just think hard about exactly how you want your protocol to work, and then code the transmitter and receiver to match the specification. If you're designing both the transmitter and receiver just pick however you want your EoT bytes to work that makes the most sense to you.