I understand that for a non-believer, for an academic, it is probably a simpler proposition to accept that this somewhat atypical practice of not pronouncing the name of God in the manner it is spelled is easiest explained as a gradually evolving taboo, perhaps influenced by surrounding cultures encountered in the Babylonian exile.
Yet, as I believe I have said here before, I find it troubling when an Orthodox Jews' belief in God and Torah isn't reflected in how he answers such questions. Here it is particularly troubling since we are not discussing a scenario which is inherently implausible, just extending the current practice known to be observed for two thousand years back another thousand years or so. If we were to suddenly discover a first Temple period writing alluding to the practice, no one's secular worldview would be challenged (although it might prove uncomfortable for some "divine name'ers").
Let us take a look at the evidence from our Mesorah:
An altar of earth thou shalt make unto Me, and shalt sacrifice thereon thy burnt-offerings, and thy peace-offerings, thy sheep, and thine oxen; in every place where I cause My name to be mentioned I will come unto thee and bless thee. (Exodus 20:21, Soncino).
A strong connection is built between the altar, i.e. the Beis HaMikdosh, and mentioning the Divine name. Rashi elaborates that permission to pronounce the Divine Name as spelled is only given at the Beis HaMikdash:
‘In every place where I cause my name to be mentioned’ Where I give you permission to mention My Ineffable Name, there ‘I will come unto thee and bless thee’ (i.e.) I will cause My Divine Presence to rest upon thee. Hence you learn that permission was not given to mention the Ineffable Name save where the Divine Presence comes, and that is the Temple there permission was granted to the priests to mention the Ineffable Name at the ‘lifting of the hands’ to bless the people’ (Sota 38)” (Rashi on Ex. 20:21)
This really is not a surprise when we reflect on it. Most of us familiar with the T'nakh can remember that Har HaBayis is frequently referred to as the place where God would put His Name:
It shall be that the place where Hashem,your G-d, will choose to rest His Name--there shall you bring everything I command you: your burnt-offerings and your feast-offerings, your tithes... (Deuteronomy 12:11, Stone Edition).
Insofar as this dichotomy between how G-d's name is written(and spoken in the Beis HaMikdash) with how it is generally pronounced is part of the original protocol for the use of G-d's name, the general pronunciation א~ד~נ~י does not constitute a "substitute" but is itself the proper pronunciation for י~ה~ו~ה!
R. Abina opposed [two verses]: It is written: ‘this is my name’; but it is also written: ‘and this is my memorial’? The Holy One, blessed be He, said: I am not called as I am written: I am written with yod he, but I am read, alef daleth. (Kedushin 71a, Soncino,Halakhah.com)
א~ד~נ~י, while having its own nuance, is not a mere substitute but the Divine Name as it is pronounced outside of the Mikdash. Similarly the Rambam writes:
There are seven names [for G-d]: The name which is written י-ה-ו-ה. This is [referred to as][G-d's] explicit name and is [also] written א-ד-נ-י (Rambam, Hilchos Yesodei HaTorah 6:2, Moznaim]
Meanwhile the pronunciation of the Divine Name as it is spelled was restricted in its use, "This Sacred Name, which, as you know, was not pronounced except in the Sanctuary by the appointed priests, when they gave the sacerdotal blessing [Bircas Kohanim], and by the highpriest on the Day of Atonement" (Rambam, The Guide for the Perplexed I:LXI (Translation by Friedlander))"It was not known to everyone how the name was to be pronounced, what vowels were to be given to each consonant, and whether some of the letters capable or reduplication should receive a dagesh. Wise men successively transmitted the pronunciation of the name, it occurred only once in seven years that the pronunciation was communicated to a distinguished disciples" (Ibid LXII).
With this in mind we can better understand the opinion found in the Mishnah, "And these are the one's who have no share in the Olam HaBa...Abba Saul says, Also, he who pronounces the Divine name as it is spelled" (Mishnah, Sanhedrin 10:1). Pronouncing God's Name as י~ה~ו~ה is reserved for the Beis HaMikdash from the time of Moshe Rebbeinu, not merely as pious attempt at avoiding taking G-d's name in vain.