@JohnnyScout, have you ever swam in a swimming pool? Did you drain all the water out afterwards, and then refill the pool from empty the next time you wanted to swim? Swimming pools contain orders of magnitude more bacteria, mould and fungus (let alone what kids also do in there) than a Sous Vide container ever will, yet we're all happy to jump straight in, getting the water and whatever is in it into our mouths, ears, and eyes. It's not uncommon to swallow some. How is this possible? That's right, pool shock. Your backyard pool can stay un-emptied for years at a time if it's properly treated, and nobody will think twice about diving in. It's exactly the same principle.
"And what if you forget to put in the Pool Shock?" Strange thing to say. You only have to put it in once, and then it's already in there.
"It's really odd that you say that pouches never have punctures." No it isn't. If you're getting punctures then you are doing something wrong. I've been cooking vacuum sealed and ziploc bagged food Sous Vide for a few years now, both with the Anova and with the DIY rig I made before that, and not once have I had any water contamination due to punctures, leakage, incorrect sealing or any other reason. Not even once. In fact the first time I've even heard of it happening to anyone is when you said it happens to you. Have you tried purchasing better grade vacuum bags, and making sure there's nothing sharp in the bag when you seal it?
But you know what? Even if it were to magically and mysteriously happen to me, I would be safe. You know why? Pool shock.
"I think many sous vide users experience that." Thinking doesn't make it true. Sorry. Come back to me with statistics and evidence.
"Frankly, this practice is not to be recommended." I tell you what's not recommended - cooking in vacuum sealed pouches that you get from the butcher. Butchers don't use BPA-free packaging, so by cooking in their packaging you're running a real risk of health damage, rather than an imaginary one. Always re-bag stuff you buy from a butcher, and the added bonus is that the leaks in their packaging won't matter any more.
Reuse your water when cooking sous vide. Doing otherwise represents nothing other than wastefulness and unscientific superstition.