In general, I think it is wise to offload to dedicated chips as much as possible, saving the microcontroller for other processing and for connecting all of the chips together. Many people disagree with that, though, and prefer to do everything in firmware and software.
It might make sense to implement all of the communication protocol in firmware if it allowed you to avoid making custom hardware. Since you have to add an external RJ45 connector anyway, though, in my opinion you might as well add a nice IC to properly handle the communication details.
Do you think EtherCAT is better than Time Sensitive Networking? Or do you have other parts of your system that require it?