Hold up a second, I'm confused: I thought we were talking using only realistic physics in this debate. You guys aren't allowed to use subspace in this discussion because it hasn't been verified as true. It may very well be possible that subspace exists in the real world, but it also may very well be possible that if anyone enters subspace they're unavoidably and immediately rent into pieces. Sure, I'll give you that the missile will not only be very visible and identifiable during acceleration, maneuvering, and evasion, and that any ship could easily enter subspace upon sight of the missile in Freespace, but within the context of this discussion we cannot assume that subspace would work as it does in freespace.
EDIT: In fact, the active sensors on the missile would pretty much announce right where it is. You'd still run into the trouble of actually hitting it, though. You figure that if you shoot it and then change velocity, the missile will change as well. So unless you maintain constant velocity, unguided munitions are completely out of the question. Even with guided weapons, their guidance system still has to get over the chaff and flare. This missile wouldn't have to worry about that so much because it's rather difficult to do that for larger ships. As for beams, that's probably your best bet to overcome this missile. Bear in mind that the farther away the missile is, not only is it harder to hit the missile with your beam, but the laser will be inherently much less focused and it will require longer to detonate the fuel in the missile. I suppose I could also say that the guidance computer would separate the KE penetrator if the temperature gets dangerously high, making a last ditch attempt to get something on target. So then you'd have to knock that penetration away, but you could do that with pretty much anything (other than laser; the particles would still collide with the ship provided aim is sure enough) because it's just a useless slug without the computer to tell it to deploy flare/chaff.