Remember that Time Flutes aren't the only way to purify Pokemon. They're an easy way to instantly do it, but they're not the only way. You can also gradually purify Pokemon over by battling with them and using scents on them. Then, once "the door to the Pokemon's heart is ready to unlock", you can visit the relic in Agate Town. That will instantly purify a Pokemon that has reached that final point. It's a more gradual method, but it's a necessary one, since there's such a limited supply of Time Flutes.