It's important not to do it too frequently, but certainly more than 1 billion people do it every day I'm sure.
People should be using distilled water or at least a proper filter when doing a sinus rinse.
This product I've pointed out is pre-mixed ocean water, it comes with the water, not just the salt packet. It's not nasal irrigation, just a spray. It's pretty effective for my sinus infections I've been exceptionally prone to.
You can also boil the water--it doesn't need to be distilled. I'm afraid distilled water may leak ions, probably shouldn't use just distilled water though I've done no research on the topic.
Based on my knowledge (science and tradition combined), you gotta use salt water, ideally the water is from a natural source and has been boiled. I don't know about distilled water. Indians have been doing this for millennia, there is a safe way to do it.
edit: Do you have a source for the fresh water being an issue? Is this an empirical result or just some theory without a study? I'm genuinely interested, I can't find any study of this. It should be easy to do as well, you could study populations in India.