One could argue that the player has the choice to inflict heavy damage on the "headquarter" of one of the factions only. Which means, he would have a choice to destroy:
- Mc Carren
- The Strip
- The Fort or additionally
- HELIOS One itself, to "disable" the whole thing.
This would limit the needed work (landscape changing / entrance blocking) to this places only. Still, it would be a lot work. It's needed to edit the endgame slideshow, you have to take care that you don't break endgame needed quests (especially on the strip?) and so on.
Now just a logical explanation is needed to justify the limited target choice. Maybe something related to the power grid? You can only target locations which are using lots of energy or something like that.
Making it possible to destroy the dam is not a good idea, as it would for sure break the whole endgame battle and would make it needed to add some alternative path for it, which is too much work for such a 'small' feature, in my opinion.
Limiting the choice with skill or other stats is pretty bad too and doesn't make really sense. Either I am able to use the weapon to destroy stuff or I am not.
/Edit: Editing the Fort would be pretty easy. I would do it like this:
1. If the Fort is destroyed, remove the fast travel waypoint to it
2. Remove the NPC at the dock, so you cannot travel to the Fort with him.
3. Remove Vulpes Incula / The other one who appears on the Strip to clean your reputation and invite you to Kaizar, if you haven't met him yet.
4. If it would be possible, add big black some trails over what has been the Fort before. Sadly, I doubt that this is possible, as particle effects are not shown in the LOD, as far as I can see (that's why the water stuff in front of the Hoover Dam is only visible if you are right in front of it [which sucks donkey balls] and also why the black smoke at Nipton is only visible if you are in or very close to the town [which sucks too])
HELIOS One is simple too:
Remove all NCR soldiers, exchange the power plant with a destroyed version, maybe also destroy the solar panels, remove all ways to enter the building.
See. Pretty easy, huh? :p