I've heard this story was not originally part of the Gospel, but was added in.
The best reason I can imagine is it shares many sentiments with Matthew 18's parable of the king who forgives the debtor, who in turn refuses to forgive a lesser debt. Is this any credit to its originality?
The true answer regarding any question about whether a given passage was in the Autograph™ or not is that we really don't know. The fact that a given passage, verse, word or phrase is in the oldest manuscript on hand doesn't guarantee that the same passage, verse, word or phrase was in even older manuscripts that are lost. By the same token, the fact that a given item might be in a later manuscript but not earlier ones doesn't guarantee that the item wasn't in some still older lost manuscript. We might infer some things about the presence or absence of an item in various manuscripts, but we can't usually (if ever) prove those things.
What we do know about the pericope of the adulteress (John 7:53-8:11) is summarized in Metzger's Textual Commentary on the Greek New Testament (2nd ed.): "The evidence for the non-Johannine origin of the pericope of the adulteress is overwhelming" (in laymen's terms, "We don't believe it was in the original"). It is missing from early manuscripts and from the important Sinaiticus (א) and Vaticanus (B) codices, both of which date to the early to mid 4th centuries (they are the oldest complete Bibles we have). John Chrysostom (c 349-407), probably the premier Greek commentator on John in antiquity, doesn't address the passage in his commentary. Nor does the latter Byzantine commentator, Theophylact of Ohrid (1055-1107). It is thought to be a largely western addition to the text, although Jerome (347-420) wrote:
In the Gospel, according to John, there is found in many of both the Greek as well as the Latin copies, the story of the adulteress who was accused before the Lord.1
Augustine actually speculated that the text had been removed by some in order not to somehow encourage adultery, as the account portrays the Lord forgiving it.2
Metzger's detailed commentary reads:
It is absent from such early and diverse manuscripts as 66, 75 א B L N T W X Y Δ Θ Ψ 0141 0211 22 33 124 157 209 788 828 1230 1241 1242 1253 2193 al. Codices A and C are defective in this part of John, but it is highly probable that neither contained the pericope, for careful measurement discloses that there would not have been space enough on the missing leaves to include the section along with the rest of the text. In the East the passage is absent from the oldest form of the Syriac version (syrc, s and the best manuscripts of syrp), as well as from the Sahidic and the sub-Achmimic versions and the older Bohairic manuscripts. Some Armenian manuscripts and the Old Georgian version omit it. In the West the passage is absent from the Gothic version and from several Old Latin manuscripts (ita, l*, q). No Greek Church Father prior to Euthymius Zigabenus (twelfth century) comments on the passage, and Euthymius declares that the accurate copies of the Gospel do not contain it.
When one adds to this impressive and diversified list of external evidence the consideration that the style and vocabulary of the pericope differ noticeably from the rest of the Fourth Gospel (see any critical commentary), and that it interrupts the sequence of 7:52 and 8:12 ff., the case against its being of Johannine authorship appears to be conclusive.
"At the same time", the Commentary argues, "the account has all the earmarks of historical veracity."
It is obviously a piece of oral tradition which circulated in certain parts of the Western church and which was subsequently incorporated into various manuscripts at various places. Most copyists apparently thought that it would interrupt John’s narrative least if it were inserted after 7:52 (D E (F) G H K M U Γ Π 28 700 892 al). Others placed it after 7:36 (ms. 225) or after 7:44 (several Georgian mss)4 or after 21:25 (1 565 1076 1570 1582 armmss) or after Lk 21:38 (f 13). Significantly enough, in many of the witnesses that contain the passage it is marked with asterisks or obeli, indicating that, though the scribes included the account, they were aware that it lacked satisfactory credentials.
Based on all of the above, the Nestle-Aland committee couldn't bring itself to completely eliminate the passage from the Critical Text, but they decided to place square brackets around it. Some English versions based on the Critical Text (e.g. RSV) place the passage in a footnote, but I am not aware of any modern versions that eliminate it altogether. The passage is in the Textus Receptus, Majority Text, and the later Byzantine Patriarchal Text, so Bible versions based on those texts include the passage; as do all versions based on the Vulgate (e.g. Douay-Rheims).
1. Against the Pelagians, II.17
2. On Adulterous Marriages, II.VII.6
Apparently, it was not. Scholars believe that it was an actual historical event that circulated in the church for several hundred years and was at last placed in its current location in the Gospel of John. If you take the story out all together, no doctrine is lost or altered, but a great deal of poignant beauty WOULD be lost.
This article mentions why this section is not original to John's Gospel.
You'll notice that many of the accounts in the Gospel of John do not appear in the other Gospels, and similarly many of the accounts that appear in the other three gospels do not appear in John.
The first three gospels were written to spread the good news of the life of the Savior to different audiences. From their content it is apparent that Mathew was writing to the Jews, providing them with references to scripture and fulfilled prophecy that proved Jesus was the Messiah. Mark's gospel appears to be tailored to the Gentiles, as does Luke's, but Luke offers his readers a polished literary account of the ministry of Jesus. John appears to be authored many years later for the benefit of the members of the church. It does not contain much of the fundamental information about Jesus that the other gospels contain. John's primary purpose appears to be to emphasize the divine nature of Jesus as the Only Begotten Son of God in the flesh. It's as though John's intent was to "fill in the gaps" and present the works and teachings of Jesus that the other authors of the gospels didn't touch on.
For a side-by-side comparison, view the harmony of the gospels. It documents all the events captured in the gospels, and lists which verses those events appear in each gospel. Apart from the event of Jesus forgiving the adulteress, there are more than 50 unique events recorded in the Gospel of John that aren't recorded in any of the other gospels, the material in John is 96% exclusive to the Gospel of John.
