Hm, really? Shows what I know about actual physics.
Right, because the pods would be going the same speed as the ship, unless the ship was gaining speed. Derp.
In that case, I don't have as much of a problem with it. The obvious easy solution would be to just put the antimatter pods below the deflector and have antimatter lines running up to the core astride the deflector machinery to a horizontal neck core. A little convoluted, but it'd work.