The barrels only contain galven coils for focusing the bolt. They have nothing to do with generating the blast itself. The size of a bolt or barrel could also be indicative of the fact the bolt is not very coherent (or, as Saxton has said:Vympel wrote: It's the barrels, not the turret, that's important. It doesn't matter how big the turret mechanism is itself, what matters is the size of the barrel- i.e. how big a blast comes out. A perfectly reasonable explanation is that the increased size of the ISD1 barrels means you need a big turret ring to take the greater recoil- which we know from Slave Ship to be in the gigaton range.
http://www.theforce.net/swtc/misc.html#combatQualification: In TESB we see that AT-AT guns have variable power settings (small shots for eliminating troops, "maximum firepower" for destroying structures like the power generator). We don't know what setting was used to attack Skywalker in Dark Empire; it might be the lower setting. Furthermore, we don't know whether the effective diameter of a bolt changes depending on the power level (for the shot against the power generator, the bolts were brighter, longer and greater in duration, but not necessarily wider).
Actually it has not been determined whether or not the effectual part of a blaster bolt has any thickness at all. It is possible that all bolts are microscopically thin, whether they come from a pistol or a Death Star. The apparent visible width may be due to nothing more than the glare spread on the observer's retina and/or movie film.
You're also neglecting the matter of the equipment required to CREATE the bolt. You can't fit those into the barrel, I might add.
Third, you're still neglecting the detail of recharge time relative to the power of a bolt. One can trade off increased time to "Charge" up a bolt to a higher output, even if your components are smaller.