Apparently, according to others on this post, the Well never gets destroyed... so, but if you still want the option, I allied with Abelas, killed the Vessel, and basically sided with the ancients in any conversation throughout that quest.
Does that help?
Sort of. Only I did the same thing (did the rituals, sided with the ancients, picked every "Morrigan back off" "this sounds bad/dangerous" option) and still couldn't get the option. I keep hearing that it IS an option but can't seem to find any definitive proof of the matter.
I'm thinking you might have to be Dalish? It would sort of make sense if an elf and not a human got to decide the fate of the well. (I also did have the "I know the wells dangers" dialogue and confirm that this still does not destroy the well).
I'm also thinking that perhaps it isn't an option though they make it seem that it is. If you think about it, if you destroy the well, and thus the key to the Eluvian, you would have no clear escape route when Corypheus busts in. Unless someone in here can tell me what the secret to destroying the well is?
But thanks for your help!