The issue of the possibility of incitement to violence by Rav Yitschak Shapira in his book "Torat HaMelech" is certainly not so clearly one of "silencing the right" or "silencing Jewish religious leaders" as many people wish to believe, and, in fact, as Rav Yoel Bin-Nun has pointed out, actually that is not at all the issue.
Everyone who wants to truly understand this issue should read Rav Yoel Bin-Nun's article at:
The article is in Hebrew, and I don't know if there is any available English translation of Rav Bin-Nun's article; but, then again, anyone who wants to discuss this issue intelligently has to be able to read Hebrew at a very high level of understanding in any case.
Rav Bin-Nun, a person who has actually read the book "Torat HaMelech" written by Rav Yitschak Shapira, makes the point that anyone who reads the book can see the opening it presents for wanton violence against other Jews (yes, that was in the book too, but as Rav Bin-Nun mentions, it was not discussed publicly at all), as well as against non-Jews (not only within recognized frameworks of war between the Jewish state and enemy states).
Additionally, Rav Aviner has also pointed out that we have never made a secret that in war situations killing occurs which would not be normally permissible, but that this does not mean that we permit such killing wantonly, without recourse to the state institutions which are entrusted with dealing with such situations. In short, taking someone's life in an impetuous manner is murder, even if you think that you can somehow justify his death as being for the "greater good".
Unfortunately, the way the book "Torat HaMelech" deals with these issues of taking someone's life can easily lead "hotheaded students" to feel that they have every right (and even a responsibility) to kill people whom they feel are "injurious to the Jewish people". Assembling together so many "Halachic discussions" relating to killing people who fall "outside of the proper way of behaving according to our authoritative interpretation of what that means"; can easily lead one to believe that the author's intention was indeed that the "hotheaded students" should feel that they have free rein to perform all sorts of abominable actions.
Even if the author did not intend that, he certainly violated the warning given in Pirkei Avot (1:11) by Avtalyon, "Sages be careful in what you say.."; and it is not surprising that the legal authorities in our country suspect him of incitement to violence.
Anyone who gave a Haskama to such a Sefer without reading it is reckless and irresponsible to say the least, and anyone who read the Sefer and still gave a Haskama shares the burden of violation of Avtalyon's warning, which is not "just a Mishnah with some advice", but a warning that this type of action can easily cause Chillul HaShem.
As someone who knows personally many of the people involved in this issue, I feel saddened that, once again, Rav Dov Lior, a man of deep Torah knowledge, has been drawn into something he should have been wise enough to steer clear of (but no one has ever guaranteed that much Torah knowledge ensures that one will be worldly-wise as well). Unfortunately, as many people who know Rav Lior well can attest, he tends to be drawn into situations which lead to suspicions of incitement; and if he hasn't learned how to steer clear of them until now, I truly hope that he will learn from the present situation to weigh these types of things very carefully (and to get proper advice from some excellent people who have been trying to keep him clear of these situations for many years), so that he never becomes entangled in such a situation again.
Since the Police have demanded that Rav Lior come in to answer questions for their investigation (and issued the arrest warrant when he refused), he should certainly make an appointment to meet with the Police and tell them that he has nothing to hide and explain the situation forthrightly to them in order to clear the atmosphere. I doubt that he actually intended incitement, but now, after so many unwise actions relating to this issue, he must first of all clear himself, and avoid such situations in the future.