The protocols issue is a fair point, though they could just be for the high yield planetary strike munitions as we saw on the Algae planet fight, but the concern over "radiological alarm" isn't a plausible argument - if you're close enough to the enemy to be using the turrets, I'd imagine there's a fair chance they'll have seen you already. 
Ummm, the final charge of the Pegasus, anybody ? 
Save your smugness - there was no indication at all that the Pegasus ahdn't been detected - the basestars were starting to redeploy. As was suggested by Angelus, Peg probably jumped in close and was able to engage before they set up a new formation - that had always been my interpretation of it, anyway.
I can't say I have looked closely enough to carry any weight to the argument, but I didn't notice many of the shells missing the basestars in engagements - they're just not terribly effictive because they're not nukes. If there are a lot of misses, then perhaps it's because Galactica lacked a fully trained crew, with many positions occupied by civilian "space fillers", and that may include the turret crews (especially after many of the crew left Galactica to colonise New Caprica).
As for the propellant/rail gun argument, I though it was settled by the muzzle flashes from all the guns in the show that they don't use rail guns. OK, it's just sci-fi, but while they may have the technology to use rail guns and the magazine safety/storage space arguments are sound, the amount of energy needed to power all the batteries (including defensive) as well as the engines, FTL, life support, gravity and so on could exceed the power available from the reactors, and of course conventional shells are more reliable - you can continue to fire them without electrical power (as long as you have manual loading and aiming capabilities) if the ship's power system is damaged...
