As Ranieri pointed out, we don't know if you need 10/100/1gig or half/full duplex. We also don't know what kind of CPU you are using. And we don't know how many of these you want to make (I'm assuming 50+, for various reasons). So this answer is sort of a stab in the dark, but...
There are four different approaches you can take. 1. Use a passive hub. 2. Use a 3-port switch chip. 3. Use a CPU that has two Ethernet ports on it. Or 4. forget the 2-port requirement and use commercially available Ethernet switches instead.
I've done enough PCB's with Ethernet to tell you that a passive hub isn't all that great. It might work in some one-off situations, but for a real product they stink. They will limit network bandwidth in weird ways, limit your max cable length, etc.
There are several companies that make Ethernet switch chips. Micrel is one of them, and more importantly Digikey has them in stock. I haven't read the datasheets to know now suitable they are, but it looks promising.
Using a CPU with two embedded Ethernet controllers can be a good option, and would be the option that most companies would choose. But for this to work well, the CPU should be at least a 32-bits, like an ARM or PowerPC. The CPU needs to be running a reasonable TCP/IP stack and be setup to route packets between the two Ethernet controllers. Companies like AMCC and Freescale make these. TI has one on their roadmap, although I don't know if it's available yet.
So I don't know which one will be a good solution for you. My guess is that you'll have to choose between the lesser of three evils, but that's frequently the way engineering works.
I see no problem in your case except the capacity of HDD is limited.
50 % of 1000 Mbps uplink is about 62.5 MB/s to store.
A 1 Tb HDD will be filled in full during less than 16000 seconds (about 4 h 30 min).
62.5 MB/s is not guarantied for an HDD as it write speed is about 50-150 MB/s (from here) therefore you need to parallel 2 or 3 of HDDs (e.g. RAID 0). Even low-cost Mini-ATX motherboards integrates two and more SATA interfaces.
Any modern Core-i3 PC could run that task. You can try/test your PC with Wireshark as a software to run the packet capturing.
A LOM Gigabit Ethernet is typically OK, but if you want stronger time stamping you could use specialized capturing hardware like the Endace DAG capturing card.
Best Answer
Pretty sure that 24V connected to pins expecting 3V or 5V is going to damage something. Starting with the magnetics in the ethernet connector.