If the military followed that logic they wouldn't have any weapons at all. All the moral implications of detonating a nuke anywhere inhabited aside, from a purely military standpoint you have a powerful, expensive weapon that you want to be able to deploy in any environment possible. Playing a guessing game as to where you'll actually need it and designing it according to that is simply not the way it works.
A military's weapons and equipment are the physical expression of their doctrinal beliefs, save where cost or politics dictate otherwise. There is a
reason why nukes are not used in the military; they're stupid. They naturally limit one's offensive, defensive, and logistical options as a result of their side-effects. They destroy the reasons why anyone would go to war in the first place; territory and resources rendered uinhabitable and unuseable. Morality has absolutely nothing to do with why tactical nuclear weaponry is a dead concept in the modern world.
In space, these rules do not apply, so one is free to use nuclear weaponry as much as they like.
I'll accept Galactica has orbit-to-surface nuclear weaponry because it's a lot easier to control a platform like Galactica through checks and balances and thereby insure nuclear weaponry is only used when appropriate.
Also, what slayer said. This exact nuke was seen in the show. Got a problem with it's design, I suggest you take it up with whoever designed it 
I'm checking again as I write this, but I don't believe that we actually did see the whole thing, just the forward two thirds. Retraction will be issued as appropriate.
The Cylons land on planets, planets are big, and whatever nuke tech they use is apparently fairly clean. The need and the ability to use the nukes in atmosphere does exist.
Which is why they gave Galactica her battery. (Which incidentally renders the use of fighters and Raptors to deliever nuclear weapons to ground-based targets redundant.)
Also, you seem to be forgetting that they made a point of mentioning there was a strong need for anti-radiation meds for both Helo and Anders' merry little band. They're not that clean.
