I admit before I begin that I have not yet read Halivni's book, all I've found is this article so I may be missing something.
Halivni's thesis, as I understand it, is that Ezra had a less then perfect copy of the Torah (we can say that the periods of the bad kings caused difficulty in its transmission or something like that) at his disposal and that he made use of a certain level of editorial discretion in order to place it together.
I'd like to focus on one of his proofs, the baraita in Avot D' R' Nosson 34:4.
Marc Shapiro has already cited it here -http://www.yutorah.org/showShiur.cfm/704648//The_Last_Word_in_Jewish_Theology?_Maimonidies pg. 200 and I'm to lazy to retype it.
I honestly don't think that this Baraita supports a theory that anywhere near as radical as that espoused by Halivni. If you look at the examples cited earlier in the Baraita, they are all relatively innocuous. In most cases, we have a passuk that isn't entirely clear and the dot is meant to stress that the sentence is to be understood in a certain manner, thus by Pesach when it refers to the a "far way" the dot tells you that it isn't very far but anything out of the Azarah counts as far, etc.
That being the case the conclusion should be understood likewise. Ezra had a perfectly whole text. What Moshe (so the Binyan Yehoshua understands it (She'Lo K'Dr. Shapiro), for what has Eliyahu to do with the text of the Torah.) means to ask is that given that the statement is unclear (far can be understood as being very far, Esav's kiss might be thought to be in earnest, etc.) he should have used the power of Tikkun Soferim vested within him (There is a nice overview of this at Seforim - here) in order to clarify the text. To which Ezra responds that rather then using the more radical method of Tikkun Soferim he chose to put the dots on the letters to signify that they should not be understood simply.
See the Binyan Yehoshua there who takes this approach. While there is still a certain level of radicalism even in this, it's a far cry from the great building that Halivni builds on top of this Baraita.
Nusach Acher - hopefully a bit clearer:
As I understand Halivni takes from this baraisa two things.
1.Ezra had an imperfect copy of the Torah.
2. He made use of his editorial skills to patch together the incomplete text he had.
I just don't think that the ten examples the Baraisa brings show anything near this. We have no reason to assume that the word "neshika" by Esav is a mistake. All the dot is signifying is that there is a deeper (Midrashic?) meaning. That applies to most of the cases. As I understand it the text at then end is merely saying that Ezra could have used the relatively minor power of Tikkun Soferim in order to clarify the texts. Maybe add or remove a word here or there. Certainly its still a Chiddush, but Halivni seems to be jumping the gun and from a few unclear pesukim he creates an text "maculated beyond repair"? From the ability to move a letter here or there he gives Ezra full editorial discretion.