Acessing Data on GMII

You don't have to modify the packets to implement PTP, you just have to timestamp them. I think that the only application that would require to modify the packets in a PTP 2.0 compliant Ethernet switch.

You are right that the second possibility is the most accurate. One way to do it is to monitor the (R)GMII signals to detect if a PTP sync packet is being sent or received. The TSU would need to detect the preamble and SFD to timestamp the packet, and then read the other bytes to check if the packet is IP, UDP, and on the correct port number. It isn't too difficult to do. It can then report the timestamp to the software layer.

I have made a PTP implementation on Nios, but unfortunately I can't share it here as it is my company's IP. For the software side you can have a look at this project: http://ptpd.sourceforge.net/doc.html