There is no premise in the rules for this. The rules for skyfire state that a model firing a weapon uses it's normal ballistic skill. All shots are fired simultaneously using the same ballistic skill (there is nothing in the rules that indicate that ballistic skill is determined on a "per-bullet" basis instead of a "per-model" one).
I can see a couple precedents for firing at a different BS for a model. This is due to thinking about how other armies deal with skyfire.
1. Flyers themselves - They can choose to use the Skyfire USR, but shots at all other targets are snap shots. Granted this is only really relevant if the flyer is a Super Heavy, but it gives a situation where a single model is firing at separate Ballistic Skills.
2. Vehicles firing after moving - This one is far more common. If a vehicle moves it can only fire a certain amount of weapons at full BS. The others are fired as Snap Fires. This happens to me rarely if I were to take a Target Lock on my Hammerhead. If I move 12" and bought a Multi-Tracker, I can fire the Railgun and one Burst Cannon. The final weapon is a snap shot.
This also applies when firing an Ordnance weapon from a vehicle. All shots besides the big gun are snap shots.
3. Hydra Flak Tank FAQ - This is the big one. When I was thinking about vehicles and their separate BS, I decided to check out the wording in the FAQ about the one tank that has Skyfire.
Here is what I found.
Page 51 – Hydra Flak Tank, Hydra Autocannon.
Add the Skyfire special rule to the Hydra Autocannon’s type.
This is probably the thing that clarifies the rule for me about using another model to fire a Skyfire emplaced weapon. The Hydra doesn't have the skyfire rule, it's weapon does. It can fire it's heavy bolter at the flyer as well, but it will be a snap shot.
I'd say that even if a crisis suit could fire two weapons. (the Quad gun and Twin-linked Missile pod) Only the Quad gun would fire at normal BS if shooting at a flyer.
Of course, I'm still willing to take a cheap upgrade on my Shas'el that would let me fire 6 Twin Linked S7 shots at a rhino.
If I were in a tournament, I would bring this to the judge and ask. Of course someone could also make the argument (weak as it would be) that a Hydra could fire its Heavy bolter at full BS to take down a flyer, but since I don't have any flyers, it doesn't hurt me much.