Read
this and replace the word beer with cider.
The whole history of beer, wine, mead and cider/Fermentation is general is that nothing pathogenic can exist in them They were consumed in places where the water could kill you, or make you sick.
Even slightly fermented beverages were consumed, even by children. Hard ciders were drunk like we drink bottled water.
Why do you think the Catholic Church chose wine as the basis of their sacrament? Because wine was more important to the culture of the desert where Christianity came from than water. Water safe, drinkable water was rare. So wine was the safer, common beverage of the day.
The reason you were in tha bathroom was more than likely that your gut is not used to all the yeast in suspension in the cider. I don't know how long the cider was fermenting and clearing before you bottled it, or if you've ever brewed anything else before, but some folks aren't used to yeast in high concentrations. Look up yeast farts and you'll see. But eventually your body will get accustomed to it.
I wouldn't expect a NORMAL grav beer to be carbed at only 2 weeks in the bottle, a high gravity cider.
The
3 weeks at 70 degrees, that we recommend is the
minimum time it takes for average gravity beers to carbonate and condition. Higher grav beers take longer.
Stouts and porters have taken me between 6 and 8 weeks to carb up..
I have a 1.090 Belgian strong that took three months to carb up.
Temp and gravity are the two factors that contribute to the time it takes to carb beer. But if a beer's not ready yet, or seems low carbed, and you added the right amount of sugar to it, then it's not stalled,
it's just not time yet.
Everything you need to know about carbing and conditioning, can be found here
Of Patience and Bottle Conditioning. With emphasis on the word,
"patience." 
Lazy Llama came up with a handy dandy chart to determine how long something takes in brewing, whether it's fermentation, carbonation, bottle conditioning....
If a beer isn't carbed by "x number of weeks" you just have to give them more time. If you added your sugar, then the beer will carb up eventually, it's really a foolroof process. All beers will carb up eventually. A lot of new brewers think they have to "troubleshoot" a bottling issue, when there really is none, the beer knows how to carb itself. In fact if you run beersmiths carbing calculator, some lower grav beers don't even require additional sugar to reach their minimum level of carbonation. Just time.
