is this the 'special rule' that allows the player to choose how much m/w/f the witchking has? if it is, then I am 90% sure the answer is no. Question: Why?
And on the point of the dragon (they com under options btw, not special rules)
Breathe Fire: Unlikely to be affected imo as it is a shooting attack. Last time I checked, you couldnt negate 'weapons'.
Fly: Pretty sure this has been FAQ'd and the answer is you can negate the flying. The model moves its standard movement as a walking model.
Wyrmtongue: Again, the bit I can see being negated is the free spell a turn. So if you negate wyrmtongue, the dragon can cast spells but must expend a will point.
Tough Hide: I dont actually know for this one. For selfish reasons I hope it cannot be negated otherwise my poor dragon is in trouble.
Also, your best bet for a official answer is to email the GW FAQ team.
gamefaqs@gwplc.comThey might be able to give you a definate answer.