I would give the edge to the Valor's fighters. However, due to the empires fighters speed, they could very well out maneuver them. If they were able to destroy the empires fighters *extremely likely due to their number and shield advantage* then they could use their missiles to aide in the destruction of the Harrower. The fighters that the Valor use, in fact, do have a very tactical edge in that they have concussion missiles, and that the empires fighters have very little shielding.
To really know how big of a difference though, we would need to include trooper weaponry, how many each shuttle can carry, and the statistics of the fighters/bombers. Don't forget that the Harrower also has many more crew/passengers that could be used to defend the ship, as well as more shuttles to land boarding parties to cripple the Valor.
