I like this idea. It's very easily something the writers could pull off and do and it has a foundation. I have my own version here: http://vampirediaries.wikia.com/wiki/Thread:791214, but to be honest I think this may be a bit better for the current situation and what the travellers are doing . I still think that Elena will more than likely die at some point, more than likely by the end of this season.
If we take some of my ideas and yours and rearrange things (I actually think yours may work best in the spot it is in--but, as to who is actually evil and creating the main issues...I think this will be a mixed bag; it may be that the worst of the worst ARE those that can come from "beyond the veil" or the real afterlife
I'm also wondering if due to the little spell that was performed on her and the fact that Katherine was also a cured vampire and a doppelganger may in fact make it possible so that IF Elena dies, she will in fact NOT be beholden to the rules of The Other Side; or it could be said that she HAS died already, but there is no way to tell since Bonnie wouldn't ever know... But, I doubt this for now as Katherine and her daughter seem to be saying things and acting more like Elena is suppressed. if Elena does die, it may be that her soul merely travels on and since Katherine has basically removed all of the magical restraints and links on Elena--that she is a vampire and a doppelganger--she may actually pass onto the "true" afterlife--or at least where humans go (but for now, we don't know where the "good guys" are located; are they in "the other-side" or in "the afterlife"). Once there, something akin to what happens in the books may partially take place. Basically they need someone to return to Earth and to act in "The Council's" stead (or whatever they decide to call it in this, be it God or even the spirits...). They'd resurrect Elena as an "angel like" creature with powers possibly like that in the book, BUT I'm sure they will be radically altered. More than likely she can fend of vampires, werewolves, and even witches...but she would be truly made to fight the new threat (again this may very well be the phantoms).
Depending on the structure of everything, it may be that the veil is protecting the world or doing something more akin to protecting those with magic--mostly witches, allowing them to perform certain magic they couldn't before. Possibly because that magic, like dark magic--which we have seen Bonnie have massive issues with before--performing this type of magic may allow a phantom to enter a witch more easily. The anchor was created to help protect the supernatural (and possibly humans as well; we don't know if they're around except for some subtle hints and we don't know what they can "feast on" yet...like vampires going for blood, phantoms I imagine will either for a magical source and possibly a soul--this is partial guesswork, so I'll stop here) from the phantoms. But it's core function may also be two fold; the second part, allowing travellers to use "expression" unchallenged and also without "morale constraints" (as dark magic seems to be a candidate right now for what is an attractor--if what Bonnie nearly got "consumed by" or merely ran into was a phantom--though some may call it a "spirit") . That is one possibility--besides the longer ones... Sacrificial magic, like we see in The Originals, used by some of the ancestral witches more than likely are using a bit of expression to not get consumed, as Bonnie had absolutely no problems channeling the entirety of ALL the sacrifices from the expression sacrifice triangle.
If it really is phantoms and the key is to do something about the anchor. No matter what the truth is, we will see a dramatic shift by the end of this season when the Augustine story-line starts to end and the next truly starts (though as we know parts of it have already begun; like taking Elena's and Stefan's blood, the mass amount of travellers coming into the area, helping Wes; I imagine they helped him simply because of a vision or a direct order and nothing else...as they had nothing to gain from it unless it was literally "destined" to happen; perhaps it was seen that Damon needed to be the way he is and that EVEN Katherine needed to do what she is doing now--which may be why they are letting the whole issue of Katherine killing a traveller, at least for now, go unanswered; IF the travellers are ALSO getting prophetic or even direct communications from "The Council" as I mentioned above--like I said, I may have the whole "The Other-Side" argument backwards, with The Travellers creating the safe haven and a place to deal with everyone's true threat...which as of yet is unknown; no matter what, Elena will end up being the "ace-in-the-hole" and I expect a large transformation for her, but who has any idea when that may happen and also who's side she will be one, until we know all the facts).
We will see soon if the travellers are helping or hurting...or like many characters, creatures, and societies in TVD...they are doing both... We will more than likely also see the emergence of the true threat for TVD by the end of this season, but it may happen half-way into next's, we'll see how they play it. I think it depends on how long they want to protract this whole Augustine and Katherine story-line (and I think both of these events are happening to force those in Mystic falls to not pay attention to the issue that is coming at them and slowly setting up around them; it may be that the travellers for an as of yet unknown reason set this whole thing up...to some degree, but they have had a hand in everything that is going down: Silas & Amara, Tessa, The Anchor, The Cure, Katherine, and now Augustine)...
Hopefully I made that clear enough as I know it had a lot of ideas.