If you asked me, I thought the Enterprise seemed better able to handle the damage than the Reliant.
Might have something to do with the fact that, while half of Kirk's crew were half-trained kids, Khan had less crew overall, and all
of them were half-trained (or full-trained but zombied out) at most.
On the balance of weapons between the two ships, we already know the torpedo situation: Khan 4, Kirk 2. We might count just the number of phaser "pimples" and assume that all of them are of equal power, in which case it's something like Khan 16-22, Kirk 18. That is, both have 12 saucer phasers in 6 pairs, and Kirk has 4 underbelly and 2 above-shuttlebay single phasers while Khan has 2 single phasers on each roll bar corner (on the sides of those cylinders), plus possibly 2 single phasers under the impulse engine (not used, but visible on the model in some pics), and possibly 2 additional single phasers on each roll bar corner (the forward- and aft-pointing barrels, although those are not seen firing and don't resemble the other phaser pimples much).
We might also speculate that the single phaser banks are of "lower caliber" since they don't see much use. But that's the only basis for such speculation, really.
Whether the two ships have identical powerplants is debatable. They seem to have the same sort of warp engine, but appearances might deceive. And their impulse engines certainly look different - Khan's is bulkier, with bigger nozzles or radiators or whatnot, and has both dorsal and ventral blue domes, whatever their function. It's quite plausible that Khan would have an inherently superior impulse drive.
Is Kirk's ship really that much heavier? The secondary hull is mostly hollow, as admittedly are the aft extensions of Khan's ship. The neck plus torpedo launcher is probably matched by the roll bar plus torpedo launcher in terms of mass.