As this will be calculation based rather than simulation based, the aircraft will know before taking off and before landing whether the runway will accomodate that plane.
You should be unable to issue an order to fly to an unsuitable airport and if the runway is shortened midflight the plane will treat the order as if the airport had been destroyed.
Im considering an acceleration model based on power and weight where planes must reach a certain velocity before take-off and therefore larger planes would require longer runways, although whether this would provide too much of a challenge for the player is really a question. And if a plane fails to take off whether the penalty of losing your plane becomes a negative point against gameplay.
I would suggest not letting the user set or change the runway at all. Just forget all this complicated mess.
The game already places every airplane in one of two categories: small or large.
So, only let the user select one of two runways to place: a short runway for small airplanes and a long runway for both large and small airplanes. Like with the current airports, if the user needs to extend a runway, he needs to demolish it and build the long runway in its place.
This will be so much easier to code and will be perfectly acceptable to most every player.
You know the old saying: Keep It Simple Stupid