I believe Wilders' position on the Koran is that it openly incites violence and therefore goes beyond the freedom of expression. He claims not to advocate violence but the right to criticise Islam. Therefore, if all the above is true, he is not being a hypocrite.
If that is the case that would seem to indicate that he agrees with the legislation which led to his prosecution, just not that he has breached those laws.
Or that he stands above that law.

The question whether Wilders is hypocritical is an interesting one. A couple of quotes, taken from the Appeals Court's
verdict.
First, what has Wilders said about the Koran:
Artikel Volkskrant 8 oktober 2007 “Wilders: verbied de Koran, ook in moskee”
- “Dit boek zet aan tot haat en moord, en past daarom niet in onze rechtsorde. Als moslims willen participeren, moeten ze afstand nemen van deze Koran. Ik zie in dat dit veel gevraagd is, maar we moeten stoppen met het doen van concessies”
In an article in the Volkskrant newspaper, October 8, 2007, titled "Wilders: ban the Koran, also in the mosque", Wilders was cited saying:
This book incites to hatred and murder, and therefore doesn't fit in our legal system. When muslims want to participate, they have to distance themselves from this Koran. I see that's a big demand, but we must stop doing concessions
The Court also noted that he has repeated the "ban the Koran" phrase quite frequently.
It's also interesting to note that, while he frequently advocated banning the Koran, he never filed a complaint with the public prosecutor to actually do so.
Wilders himself has also been heard by the Court:
Ik vind dat ik de ruimte heb en moet krijgen om te zeggen wat ik wil, waarbij ik me realiseer dat des te uitgesprokener je bent, des te meer reacties je – zowel in positieve als in negatieve zin – krijgt. Als volksvertegenwoordiger vind ik echter dat je alles moet kunnen voorstellen.
<snip />
Mijn overtuiging is al met al dat ik binnen de kaders van de wet ben gebleven.
In translation:
I think I have and should get the privilege to say what I want; and I realise that the more outspoken you are, the more reactions you get, both positive and negative. As an MP, I think I should be able to propose anything.
<snip />
My conviction is that, all in all, I have remained within the limits of the law.
So he flirts with both notions: that on the one hand, he is allowed to say anything, and on the other hand, there is a law which says there are limits.
In various public statements during the last couple of years, he has always defended his comments with the freedom of speech. I can't remember if he ever said that that freedom was absolute.
His lawyers also filed a brief with the Court, and they are more cautiously (surprise

):
Ten aanzien van de vrijheid van meningsuiting brengen de gemachtigden naar voren dat een publiek debat over zaken van algemeen belang slechts in gevallen van uiterste noodzaak mag worden beperkt.
In translation:
W.r.t. the freedom of speech, the lawyers state that a public debate on matters of public interest may only by limited due to extreme necessities.
I think, all in all, that there is a certain hypocrisy in Wilders' stance. One way or another, he wants to be able to say what he wants for himself. When push comes to shove, he tries to hide behind his immunity as an MP. I remarked earlier that I thought he had a good point that it would be bizarre if he could make certain statements in Parliament with impunity, but not outside Parliament, but the Court has a better one. Their decision that the public prosecutor should prosecute Wilders for incitement of hatred is not only based on the content of his statements, but also on the frequency with which they were repeated. When he had repeated his "ban the Koran" comment in Parliament in, say, a debate on the price of cauliflower (to borrow from Stephen Sackur), I'm pretty sure the chairwoman would have called him to order, and the comment would have been stricken from the record.