So the author of the article appears to have read the Koran and
is to the view that he is saying, "The extremists are a relatively
honest bunch who are merely passing the bigoted Koran unadulterated
to the Muslim masses." The assertion is that the Koran is the
source of their doings and the terrorists are relatively innocent,
the by-products. Muslims have knowledge of this bigoted Koran and
just somehow developed this ability to ignore human values and
become life-size fart bombs. Meh. I'm pretty miffed he has painted
the situation that way.
I don't agree with everything that was said there, but I certainly
agree with much of it, and much has already been said. It is what
it is and I lack any capability to explain more, unlike what
Gendaken has done. However, I still maintain that the prevailing
fanatic idealogy is a misrepresentation of Islam that arises partly
from the literal intepretation of the Koran as the absolute word of
God and that doesnt mean I'm absolving Islam of its faults and
troubles. For the literalist, Islam seems to invoke a lot of
violence and wrongdoing. As a Muslim myself, there are verses in
the Koran that I feel very uncomfortable with. But literalism
shouldnt be placed much emphasis in the first place. The Holy Books
were meant to be thought about. The lady saint Rabia used to cross
out verses from her Koran which she didn't agree with because "her
God" could not have said those things.
I am also for the religious reformation and actual education for
the indoctrinated community. The activity of understanding the
Koran according to the context in which they originated, etc etc
(except some in the article) - actually, has been the practice of
Sgrean Muslims all along as far as I know.
That is how an Sgrean Muslim reconciles, lwflee? 
--------------------
I hope now to address some issues concerning Islam's tenets put
forward by the article that are the two main causes for extremism.
The rule of abrogation and the dividence of the world into two
parts, Dar al-Islam (abode of Islam) and Dar al-Harb (abode of war)
.
1. Rule of abrogation.
The concept was invented as a result of a poor understanding of the
Koran. It has been negated far long ago. The scholars base their
claim on a corrupted translation and intepretation of the verse,
which is below.
"Whichever revelations We abrogated or cause to be forgotten, We
substitute something better or similar: Knowest thou not that God
is capable of all things?" 2:106
This is the abrogation verse which is from a chapter in
continuation on the topic of past prophets and their Holy Books,
for example the Torah, Psalms and the Gospels. Here its stated that
God substitutes them with something better or similar, indicating
the Koran. It wasnt about the
verses within it. Therefore, the earlier peace verses arent
abrogated and still are very much upheld. And still on the past
Holy Books, they must be honored as ever, for in another later
passage, "Why do they ask you to judge among them, when they have
the Torah, containing God's law, and they chose to disregard it?
They are not people of Faith." | "Subsequent to them, we sent
Jesus, the son of Mary, confirming the previous scripture, the
Torah. We gave him the Gospel, containing guidance and light, and
confirming the previous scriptures, the Torah, and augmenting its
guidance and light, and to enlighten the righteous." | "The people
of the Gospel shall rule in accordance with God's revelations
therein. Those who do not rule in accordance with God's revelations
they are the wicked."
That is as far as I understand.
2. Dar al-Islam and Dar al-Harb
There is no mention of this concept in either the Koran or Sunnah.
They were products of the Jurispundence (called Fiqh) in the middle
ages when the Islamic state expanded and faced several issues about
their concise borders which were often very bloody. More
definitions were coined, Dar al-Amn (abode of security), Dar
al-Sulh (abode of treaty), etc. This classical theory bears the
stamp of those times, and it was never universally accepted even
then, for not only it sounds imperial in tone and triumphalist in
vision, the assuming of an eternal conflict between them are
morally problematical and politically untenable. It has been made
long defunct too by the successive jurists and scholars, for
circumstances and structure of life has changed.
That is as far as I understand again.
Old and obsolete components of history are being propogated and
sealed back into the religion. 