We've yet to decide whether the spy will have a +stealth command key that lets him run / move quietly for a short period of time while disguised.
Some things to be aware of: If the spy makes less noise when landing, it'll be a dead giveaway while disguised. Hence, sometimes the spy would want to make noise, other times he would not. E.g. if you jump down the 2fort lift and don't see anyone at the bottom, you wouldn't want to make noise. If you see a soldier there, you would want to hit the ground and make a regular noise.
I can't really think of any reason why the spy shouldn't be in stealth mode while undisguised. The problem is deciding whether he has stealth mode (or parts of stealth mode like silent falling) while disguised, too.