As far as rockets destroying the runway, this should only happen with a vertical launch. Launching horizontally, like a spaceplane, should be allowed. Simply making the runway be very sensitive to heating should work.
Atmospheric Fluid Spectro-Variometer isn't available until relatively late, so I'd substitute only requiring the barometer. Variometer scan could still be required before crew are allowed to EVA on other worlds.
Otherwise, these look like good suggestions, though I'd also add in a more realistic tech tree progression. Basic aircraft and unmanned rockets first, then crewed missions later. A lot of the science parts would have to be moved a bit earlier in the tree as well in order to support the idea of requiring those scans in order to be able to plan out the mission.