That's certainly something which could be coded into OpenXCOM....
True. I'll have to post it in suggestions.
Meanwhile...
One way to realistically rebalance the missiles would be to either drastically decrease the scout ufo's hit-points or to increase Avalanche's damage so that it would always destroy scouts.
Why?
Let's take a look at RL equivalents of the missiles:
Stingray:
AIM-9 Sidewinder. Whole missile weights 85kg and the warhead weights 9,4 kg.
Avalanche:
AIM-54 Phoenix. Whole missile weights 450kg and the warhead weights 61kg.
Stingray's warhead is heavier than a whole Predator SRAW missile together with launcher. I'd assume that Large Rocket's warhead would weight about 2kg like in case of RPO-A.
I'd say that a direct hit with Stingray should breach the hull like a blaster bomb and probably force the UFO to do a controlled crash landing.
On the other hand a hit with with the Avalanche would probably cause a massive hull breach and throw the UFO off balance causing it to either fall apart or crash without control and be destroyed.
So, with Avalanche, it wouldn't be possible to recover the scouts at all which would make Stingrays more useful.