So if a ship with tractor Beam tokens on it wishes to fire its Proton rockets at its target will the attack value added be the ships usual agility rating or its reduced agility after taking the tokens into account for that round?

The latter.

The Tractor token reduces your agility, which affects the calculation for the number of dice for the Proton Rocket.

For example, Gemmer Sojan would still fire Prockets with 5 dice if previously hit by a Tractor Bean but within range 1 of an enemy (2 base Procket + 3 Agility [3 -1 from TB + 1 for GS's ability]).