as you suggested, raspberry pi is way to go, use two of them in sync, much cheaper than dualhead.
there are plenty of open source video players for RPi, notably
it should be easy to emulate the synchronizing communication within vvvv either by sniffing the communication packets of player application or analyzing the source code. add your desired gpio functionality ftw.
I did setups with more synchronized RPi, my impression was that the playback triggering had sub frame duration latency. This could be influenced by the codec as well. I needed no knowledge of Python (might be needed to add the GPIO functionality), just bit of googling to set the environment (startup and so on).