The article is describing a form of quarantine much more severe than keeping people in their hotels. They're talking about cordoning off the entire affected area - basically, the area around all infection sites becomes one big border with armed guards that only allow food, water, and medical supplies in, and nobody out.

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?