Food safety with broken glass in dried tomatoes

I would recommend using Whiskey Stones. They are used in whiskey instead of ice cubes. So they should be heavy, won't rust, and are supposed to be immersed in liquid that you'll consume. I think that probably meets all your criteria.

Whiskey Stones

Another alternative is to use a rack. This comes with the Sous Vide Supreme and I find it quite useful for keeping meat submerged. It does however only accommodate certain sizes of meat. It works quite well. You can buy it separately online for $12.

Virtually every case of botulism ever recorded in the past 50 years is due to improper home canning. The risk of botulism from a commercial product is so low that you literally have a better chance of being struck by lightning and almost as good a chance as being struck twice in the same year.

There are 145 cases reported in the U.S. each year and 65% of those are infant botulism, 20% from wounds. It's hard to get statistics on infant population, but there are 314 million people in the U.S., so I estimate the chance of getting botulism from food there to be 0.00000692675% in any given year.

You may not live in the U.S., but unless you live in a country with extremely poor or nonexistent safety standards (in which case you have more important things to worry about anyway), I'd advise you to stop worrying. You are about 20 times more likely to die in a fire and 200 times more likely to die in a car accident.

As far as the spores go, they generally aren't dangerous to healthy adults, they affect infants and those with depressed immune systems, hence the heavy proportion of infant botulism cases (often from honey). That's why the WHO warns people not to give honey to infants under 1 year old, but doesn't advise any similar precautions for adults (The reason for no advice for adults is that their stomach is acidic so the bacteria cannot grow and produce the toxin. But infants have lower acidity in their stomach and botulism bacteria from honey can grow there. Honey always has the bacteria. )

Botulism spores can only be killed at extreme temperature, i.e. above 120° C. Boiling water is 100° C, so don't even try to kill them this way. You would need a pressure cooker at very high pressure, and this is why low-acid foods must be pressure-canned; simply boiling is not enough. On the other hand, the botulism toxin is denatured at 80° C, so boiling anything for a reasonable time will make it safe from botulism, but not necessarily from the many other bacteria and/or toxins that can be in spoiled food, such as those produced by certain e.coli strains.

There are plenty of things to worry about with commercial food - salmonella in peanut butter, listeria in lettuce, listeria in spinach... the list goes on and on, but one thing that's generally not on it is botulism, and I think the constant attention here on it actually makes matters worse by taking attention away from other, more common and equally serious issues. Seriously, one person died from contaminated homemade ham and now you're afraid to eat commercial mozzarella cheese?

If you aren't an infant, don't do home canning or home food preservation, and refrigerate your food properly, you're not at risk for botulism. Period. You are, however, at risk of so many other things, and really should try to learn more about food safety in general - from which you'll definitely learn facts such as boiling for 20 minutes won't make spoiled food safe.