Notwithstanding that the next Vuelta is still 11 months away and a lot can change in that time, there are a few things that they can do.
- no MTFs on climbs with multiple access points, enabling security forces to restrict access to the mountaintop (so expect a bunch of climbs like Peña Cabarga, Lagos de Covadonga or La Pandera where there is only one way up and a clear checkpoint that can be used)
- use Andorra to their advantage, we could have a stage like the 2015 one Purito designed and another MTF there.
- minimise stages hosted in the regions of Spain's internal nationalities - Catalunya, País Vasco and Galicia - as these regions' histories tend to make them hotbeds of protest of such causes. If using Andorra, they would almost certainly have to access via Catalunya one way or the other, but via the much more sparsely populated western part of the region which would be less accessible to protesters
- don't finish in Madrid, or at least not in Madrid city centre. In this case, the proposed Canarias stages, if all goes according to plan, would be a benefit, as although they have been protesting overtourism in recent years these are much less likely to be on such a scale or turn ugly, being a general cause rather than having any specific targets at the Vuelta
- perhaps utilising other sporting infrastructure, most notably motor racing circuits, to enable control of spectator access to stage finishes as well as the circuit gates giving a clear alternative timing point in the event of disruption. There are a lot of circuits in Spain that can be used including some that are near to big cities which may be the best option for involving such areas or cities while still being able to secure the stage finish (e.g. Cheste, outside Valencia, or Jerez de la Frontera. I don't know what state Jarama's circuit is in nowadays but that may be an alternative finale around Madrid)
- utilise multiple laps of a shorter course in ITTs and TTTs in order to require fewer roads be secured for the purpose
- if stage finishes are able to be secured in this manner, have alternative routes prepared for deployment if there are reports of protester activity on the way.
I don't claim that any of this would be perfect in any way, and it certainly places some restrictions on routing possibilities and would create some hassle in terms of cost of arrangement and deployment, but with 11 months at their disposal I think there's plenty that can be done to react to the disruption of the 2025 edition. The Vuelta has dealt with worse in the past, but it was before the Vuelta was as big a deal as it is now, and it was more geographically restricted in its impact back then.