Have all children in civilised countries educated in non faith schools and ban the attendance to more than ~5 hrs a week of these new faith colleges. Encourage rational, open debate about religion and morality. From a young age show Islam, Christianity, Judaism, Buddhism, Sikhism, etc. in reformed RE classes. Teach children that there is a clear divide between the society when these books were written and the laws we live under today, and encourage them to only follow parts of their religion that agree with the law of the land they live in.
And I realise this is impossible but if I could I would make certain sections of these holy books illegal. Like the ones that support domestic abuse, slavery, murder, paedophilia. It's disgusting that the books people hold most dear to them have this kind of content.
I'd also impose huge sentences on anyone connected to terror attacks or plotting one. Too often we hear of terrorists 'known to police', who were questioned and let go, and later commit atrocities. But instead of the poor system of incarceration we have now, it should be forced education. Serve your sentence but you can only get out if you understand what you've got yourself into. Which really should also count for murderers, rapists and the like, too.