The reason this is controversial is because there are close to 2 million people in the affected districts, and only about 500 of them currently have Ebola. At best, you're severely inconveniencing 99.975% of the population, and at worst, you're leaving them to die. It'd be like cutting San Francisco off from the outside world, with armed guards on the bridges and San Bruno Mountain, because measles was found on BART.
I don't know what the situation in Gabon was like, but as I understand it they depended upon local quarantines of villages, and didn't close the border of the whole country, right?
"Its size is due in part to weaknesses in the affected countries’ health systems and a lack of trust in the health workers who are struggling to combat the virus" [0]
Not sure the reliability of this source, but "The health security situation is worsened by an apparent lack of trust by the local population in their own governments and medical staff. Warnings against the consumption and selling of bush meat for instance have largely fallen on deaf ears with an inherent belief of the local populations that Ebola either must be a myth or a scam on behalf of corrupt politicians to deprive them of their most basic needs and livelihoods." [1]
[0] - http://www.intrahealth.org/page/ebola-outbreak-underscores-n...
[1] - http://www.securitynewsdesk.com/2014/08/12/ebola-west-africa...
It is difficult to educate a population in this situation about hygiene. Let alone asking them to not eat bush meat.
Searching for 'BBC Ebola' is now a thankless task - so I can't find the reference.
Now suddenly quarantines are being presented as the smart thing to do...
There are all kinds of things done in some places that have not been seen for centuries in other places.