For sure, Chlorine dioxide is toxic, that's why it is used to treat water. That treatment is probably a necessary evil as things stand now, but that doesn't mean it's the optimal solution, hence all the filtration systems you can buy for your home to filter that out.

Gut bugs play a huge role in maintaing health, so it behooves us all to keep them healthy, and minimizing their exposure to Chlorine dioxide for health reasons seems obvious to me.

Still, when chlorine dioxide kills a bug in water it converts to chlorite, which is also toxic. So while you won't get sick from the bug, you do ingest some nasty stuff in the form of a very powerful oxidant. At the very least I would want to take a dose of antioxidants with it. A packet of emergen-C would be good. I take those everyday anyway, and bring extra when I'm backpacking, but that won't protect or replace your good gut bugs. Drinking good, untreated water might though.

I have to add a bit...

The good bacteria in your stomach is like a first line of defense against any bad bugs you might ingest. You need to keep them healthy. Taking probiotics is one way, eating yogurt with live cultures, kimchi, sauerkraut, raw fruits and veggies, etc.

What kills those good bugs are things like antibiotics, chlorine, and probably soft drinks that contain sulfuric acid, like Coke. Antibiotics are the worst, and the stronger they are the harder they are on your good stomach bugs.

So, if you've taken a round of antibiotics, then head off backpacking and are only drinking water treated with Chlorine dioxide or iodine you could be very susceptible to getting nailed by those very few nasty bugs, rather from water or personal hygiene or any other source, whereas with a healthy gut you'd never even notice you got any, your gut would fight them off with ease.