Excellent stuff, so it sounds like we should add atomar lasers to the tech tree! 
I think it could already be in. The trans-newtonian tech might come up with new materials, but otherwise it is straight forwardly impossible to ever have a gamma laser, because what material would you build the focal of to reflect light of this kind that is famous for its piercing nature? ...And also because a lame infrared+other lasers could not possibly shoot this far, while it would also be kind of anachronistic to just research infrared laser when we are already flying into space... . It only all makes sense if they are trying to find an infrared application of an atomic laser.
...Not that I would acknowledge that this much thought has been put into the matter for real. Hell, despite several reports in the Bug thread (one coming from me), the description of the laser wavelength tech still falsely says the range becomes better if the wavelength increases .... while any technical progress works to reduce the wavelength instead.
I think one can come up with good explanations on its own though.
I am with you on some of the actual issues around dispersion. I actually looked at that years ago when the whole debate about "nukes in space" arose. My conclusion is that if you are restricting the effect to both radiation (which you guys have just shown is iffy unless the armor is breached) you are left with thermal effects. Thermal is actually pretty good, the vaccum of space is actually a very poor conductor for heat, so immediate concentraton is actually pretty sustanabile, and then you have the secondary effect of "roasting" a target by heat loading his systems beyond the capbabilty of his tech to disperse the heat via some sort of heat sinks.
Overheating is indeed one of the greatest challenges of space travel. I think specialized overheating weapons might again fill the 'lameness' criterium of weapons
, but it is certainly a frightening and plausible weapon possibility.
The down side is that a battle with a lot of nukes getting thrown around is A) going to play hell with EM and thermal sensors, as the radiation and thermal effects will take a considerable period of time to disperse, and B) you are leaving pockets of extreme heat laying about that act as a thermal minefield for ships moving through the target area. Direct pursuit would be VERY dangerous in such a scenario.
I must confess I have no idea what nukes actually leave behind, but my educated guess is that given their reaction comes from relatively few concentrated 'ignition' mass, there would be no medium left to condensate such energy locally. All the released power just comes out as either neutrons or gamma burst, or other EM i think, so the field of thermal threat would disperse almost instantaneously.(?) Or would the local small cloud of radioactive particles indeed already be enough heat hazard
Things will be different for sure however when firing into dust clouds or asteroid fields.
Dispersion of the effects from the warhead would be spherical, and inefficient as hell, so I guess you could agrue that the tech improvements to warheads would be both a matter of yield for volume and/or an improvement in focusing the energy into a more efficient pattern. For example, a sufficiently powerful magnetic field could act as a virtual liner, in effect producing a nuclear shape charge, which would be far more effective than the omni-directional blast of the basic warhead. This would in turn lead to smaller loads of fissile materials in the warhead to produce the same effect, netting out Aurora's smaller, more effective missiles.
I certainly like the idea. I see though that there would be an eternal competition of protection against focusing by this. If you had the means to 'contain' a massive energy release explosion so much that it can be directed (does not matter if through material or magnetic or whatever), you would far more easily become able to develop protection against it. It is basically how there is a (explosion guiding) pistol and a bulletproof vest, a tank gun and the tank armor. As soon as you have means to guide raw force of nature, you can also protect against it. If nukes could be "tamed" too, they would just degrade to becoming the next gunpowder. Not that this would really put a bar on the idea, because lower tech enemies will surely feel the effects of more concentrated force.
The entertaining thing about Aurora is figuring out where the physics stops and/or starts and the handwavium begins. 
I find it amazing that often a singular discovery could completely reshape the technological cosmos and all the possibilities the have yet. We have seen that in the past with steam engines, electronics, or lastly semiconductor tech - often a quite simple principle that we discovered that resulted in a wave of applications to totally change the face of all. If we would truly find means to overcome impulse physics in a certain way like Aurora suggests, it is fun to think in what a world that would result, which logical other applications suddenly have to arise (e.g. instantaneous wireless communication, or perfectly conserving and highly energy dense fly wheel capacitors). What would it change if we would figure out the nature of how some particles can be intertwined despite being possibly lightyears apart? Lots.
Actually, now that we're on that topic I would like to say that it would be sorta neat if you could temporarily blind scanners with a powerful nuclear burst. In my fiction, this is a tactic that was employed by one side of a battle, and I really think that having a bunch of big explosions go off right in front of you should have some terrible effect on your ship's ability to see other ships.
I subscribe to this idea.
But I would like to have sensors with EM resistance to apply their check here too. Maybe widen the definition of the nature of the "resistance" here for this sake.
