You MUST get the rust taken care of and prepped before attempting to paint. If it's nearly impossible to sand the rust, look at having the frame sand blasted. Is there a reason you don't get the entire frame painted? If it's a matter of cost, it may be more costly to have someone attempt to bend in paint with a airbush than for them to just respray the entire frame. You have to consider that time is money, and blending paint takes more time and skill than just spraying the entire thing.
With that said, you CAN airbush the problems, but more than likely the work will look like crap because your blending old and new paint, you have to get an EXACT paint match (one slight shade off and it will pop out), and then blend it well which takes a lot of skill to make it look good. It can be done, but it's either going to be cheap and look like crap or expensive and look ok...
If you want it to look great your going to have to spend the $ to have it painted properly. It's about $50-$75 to have the frame blasted, and I was quoted $200 for my frame to be primed and painted with 3 coats of PPG paint plus clearcoat then baked in their oven by a local VW/Audi dealership (the paint/primer is provided in the cost). I was told they would charge me $125 if I provided my paint. You can always get quotes and they may be less or more than mine. I suspect mine was a little higher because it is the VW dealership that is going to paint the frame using all their tools, paints, and man power. I was also told that if any of the metal needs worked on due to rust it would cost more (so keep that in mind if your bike needs bondo for rust repair). Most places will be able to give you a ballpark quote if you take them the bike or photos.
Best of luck to you!!!!