This goes beyond free speech. We would not allow terrorists to wage war physically in our country. Nor should we allow them to organize wars and recruit over the internet. Some things are more important than free speech. Free speech does not include plotting to kill others like the terrorists do.
It does not take a genius to figure out that the US government most likely does it anyway. Furthermore, free speech does not exsit, it is regulated through liable laws etc. These sites are inciting violence and as such is legitmate target.
I would go further, it is also legitmate for the USA to conduct full IT war against their enemies.
We should allow the government to block threatening websites. Generally freedom of speech is fully covered by our laws until one starts provoking or encouraging violence. That is where these websites fail to get protection for freedom of speech and head towards the blocked media category. They do not serve the public except to incite violence.
The US government itself shouldn't block them unless they are using the website for criminal activity and not merely expression of views. But if these jihadist websites file complaints about private hackers such as Anonymous and prosecutors just decide to ignore those complaints then that's OK by me. Prosecutors have limited resources and so have to decide what cases to prioritize after all.
The government should not be able to block those websites without receiving a report or complaint from someone that points them directly toward that website. Them just snooping around the WWW, finding and blocking these websites, is dangerous. What if a liberal government were to start labeling conservative websites as terrorist? Or the other way around? The government can just go on and censor them? No way. There needs to be some kind of genuine report from the citizens in order for the government to take precise, pointed and prompt action to block or censor these websites.
The US government should not censor jihadist websites. the US government should not be in the business of censoring anything. It's a slippery slope when you start allowing the government of a country whose laws are predicated on free speech to dictate whose voices get heard and whose don't. See the IRS's recent targeting of conservatives who disagree with the government's current makeup as an example.
Blocking access to private websites should be deemed illegal, and will only result in information being passed in more subversive manners. Blocking access to information does not stop an idea. At least with a website running, it is possible to track what goes in and out. Block it, and people will find new areas to exist.