Yes but it wasn't pure when we first pumped it out of the ground, either. I'd bet natural gas has a lower percentage helium than "balloon air." We are able to purify helium.
I expect the difference is that when extracting helium from natural gas, the volumes are huge and therefore the purification process is economically feasible.
Trying to do the same for small amounts of helium collected here and there is possible but not economically feasible. It makes more sense to use it as balloon gas.
It also costs energy to extract helium from natural gas. If running out of helium is our concern, then the balloon air is a source of helium we can exploit just as well as natural gas. It's not like we have helium wells pulling pure helium out of the ground.
