On the issue of Klingons not taking prisoners, it's probably a bit of outdated propaganda (Klingon or Starfleet) for our ST2 heroes, used tongue-in-cheek by Kirk to lighten up the mood of the simulation.
However, in TNG "Heart of Glory" we meet two Klingons who actually believe in that propaganda! It seems that those who take their Kahless too seriously are actually obliged to go without hostages or other captives... It's the "honorable" thing to do, and even though Kahless himself would probably have laughed derisively at the idea, his followers might well have codified it into their set of rules-that-keep-bored-warriors-at-bay-and-properly-obeying-the-priests.
On the issue of having a military presence at Genesis... What for? It's not as if anybody could come and steal the planet. Or that anybody would benefit from bombarding it. It's not capturable technology, it's just the detritus from using the tech. An invader would have to spend months painstakingly analyzing the place to even begin to divine the secrets of how it was made; not something one could achieve by barging in with a warship.
Kruge's attack made no sense, and would not have given him the "secret of Genesis", which was wherever Carol Marcus was, thus (probably) not in the Mutara Sector. Preparing against such an attack would have made no sense, either.
Timo Saloniemi