in 5.1 if you are NOT using SRM and are using VR "standalone" then traffic will always go via the appliance at some point. this is one of the downsides of using VR standalone i.e limited to one appliance per vCenter in this kind of design. So even after performing the initial sync task ongoing replication deltas would still have to go via site1 to get to site3 from site assuming you have the appliance located at site1.
the good news is this WILL change in 5.5. In 5.5 we will allow you to deploy > 1 appliance with VR even when used in standalone mode. This will mean in your example you could deploy 3 appliances as a minimum so one at Site1, one at Site2 and another at Site3. Now when you configure replication from Site2 to Site3 you simply select the Site3 appliance. Once up and running replication traffic will now flow from Site2 to Site3 for VM's configured that way and will not need to route back to Site1.
As a shameless plug we actually covered this 5.1 limitation and then later on showed the 5.5 new option in a vmworld session that myself and a colleague delivered last week in San Francisco, second session in this list:
VMworld.com: Top 10 Sessions
