At this time, no as one of the two currently available crystals are needed for two separate quests, so in the end, you'll use both of them.
Some background. Not too long ago only the fire crystal was available but after a recent update, the frozen crystal was added, along with the Master's Laboratory quest, which also requires a crystal. A future update will add a third area (lightening if the pattern holds) and likely a third use for a crystal.
There's some SPECULATION, supported by small in-game details, that sometime in the future, one of the three orbs (or the shadow orb for those that kept it) can be used to infuse a weapon with elemental damage. If, and when, that happens, it's unclear where the new weapon would fit into the current weapon tiers (stronger or weaker than the current top tier in the Ashen Wastes?).