In a nutshell the UK CAA cannot tell the MOD or MAA what to do, cannot dictate that they reconfigure the runway, change the infrastructure etc. However, the CAA can and indeed are oblidged to tell civil operators what to do and impose as they see fit any additional limitations on use considering any non-compliances with 'normal' expectations were it a civil, licenced aerodrome under CAP 168 rules.
Nothing physically needs to change if the MOD don't want to change anything, but if the CAA feel compelled to do a bit more than just highlight the obstacles, safeguarded clearances, RESAs, etc. alone and let the pilots/operators decide if they're happy to live with those non-compliances, they are now at liberty to do so.
Before last week, the CAA mistakenly believed they could not impose additional conditions on use of a Government aerodrome but now it has been made clear they can. So, assuming they accept that there are some fundemental non-compliances were it assessed as a civilian aerodrome, it is quite likely that they will now impose some constraints in use for civilian operations. As to what those might be and how constraining they could be, we wait to see.
If it transpires that due to the RESA non-compliance, the CAA dictated that some consideration should be made to applying an addition reducing factor on runway length, it is an option for the MOD presumably to reconfigure the arrester beds with EMAS instead of Lytag and may get to a point where the CAA are happy not to ask civil operators to add an additional reducing factor to the runway length. The question there is whether the MOD have the funds or desire to spend that kind of money to retain the throughput of civil business aviation operations when they don't need to do that for their own use by military operations. Chances are the funds will not be made available and so the allowable runway lengths for civilian use might remain for the time being whatever the CAA deem appropriate.