I think people are still missing the point, nothing physically changes at NHT, it's still fully controlled by the MAA (MOD), will remain so, and civil aviation can access just as they have always done.
The big difference post this case is that the UK CAA can, if they wish, now impose limitations on use on the aircraft operators - not the airport. Its up to the CAA now to decide if the use of NHT by civilian operators warrants the imposition of some specific limitations on use that apply to NHT in an effort to mitigate against the additional risks that exist at that specific aerodrome.
It will be interesting to see how long the CAA now take to decide what, if anything, they may impose on civil operators using NHT. Having not realised they had that power or obligation since 1982 under UK law, until this case arose, perhaps they wont be in such a rush. On the other hand, there could be another Learjet overrun tomorrow morning, so my guess is that they might act swiftly.