Well, we saw in "The Hub" that baseship missiles can be used to intercept incoming fire. It was only used against other cylon missiles, but it would probably be possible against a colonial shell. More difficult, since battlestar fire travels faster than cylon missiles, and are typically fired at closer range, giving the cylons less time to react, but they could do it.
The baseships' greatest defensive asset seems to be that their missiles have the longer range, and the battlestar has to devote most of its energy to defending itself from raider strikes, so the cylons can force a standoff outside the effective range of the battlestar's weapons.