I am certainly no expert in this area but this is my understanding.
Let's consider an analogy of electrons. There are low energy electrons that move reasonably freely through a lump of iron for example. The electrons in it are not harmful, we can even eat this if it is small, in fact it is nutritious. We wouldn't normally call these electrons beta particles. Then there are high energy electrons released by a nuclear process. We call these beta particles, and they can smash through numerous atoms, causing many random chemical changes. This is a cause of radiation sickness and possible death. As you can see these have completely different characteristics because of the different amount of energy they have.
The situation is the same for ions. Common, low energy ions, trapped in a chemical substance, for example sodium ions in water, are very different from a high energy He2+, liberated by a nuclear processes, not bound up in a chemical substance.
Ultimately the important difference is physical rather than chemical.
There is one other aspect: ions like Cl- are only safe when they are in a substance that is neutral overall (for example Cl- with Na+). If you were to be exposed to pure Na+ it would be extremely harmful.