I agree with your points, but ultimately the bible/quran/etc is fiction even though the advocates don't advertise them as such. This isn't so much a problem with the content of the books, but the mindset of the individual's reading these works of fiction.
And no one is allowed to advocate murder anyways. That's usually frowned upon and investigated, at least in good ol' US of A. Sadly not every country across our great disc is the USA, so some places are more lenient and/or tolerant of hate speech brought about by religious text. This is also where we get into things like Christians saying "oh that part is outdated and no longer applies lol" or "no you're interpreting it incorrectly".
All hate crimes, whether religiously motivated or not, should have appropriate punishments. However, I don't think religion is going away anytime soon if ever due to that little bit about freedom of religion and freedom of speech, which sometimes can be more detrimental than helpful, especially in the cause of Islam. But I'm not going to pretend that Islam is the biggest offender, because Christianity, Judaism, and others were just as violent at some point in their histories.
Also, banning certain parts of religious texts is not going to change anything. People will still cling to the old ways.
The problem with religion is that it was conceived to begin with, now it's going to be very difficult to do away with.