I'm so sorry to read of this. I don't understand what a "possible" kidney stone is. Did a radiologist read the ultra-sound images?
I am not fond of current medical practices or the roles that Big Pharma and corporate greed play in its current state. But, I'm going to say this with all sincerity: the only "natural" treatment for this baby is to see a licensed and certified Doctor of Naturopathy. All else would be taking a serious chance on your toddler's life, especially acting on advice from an open, public, online forum. What would happen if someone gave bogus advice and something dreadful resulted?
Unless the foreign body was diagnosed as a kidney stone, further testing needs to be conducted to determine exactly what it is. The issue here is that treatment for one condition (unconfirmed) could actually exacerbate a completely different condition (also, unconfirmed). Since this is a baby, it can't tell you whether they're in pain, or not, but 5mm is a pretty fair-sized object. I would be much more concerned with the fact that there apparently is no associated pain.
I would strongly urge you to get a final diagnosis - visit different doctors until you receive a confirmed diagnosis, and then proceed using good judgement and sound wisdom.
An adult has the opportunity to make their own decision with regard to every facet of their lives. A child, on the other hand, has no advocate other than their parent(s) or caretakers. Leave this matter to the professionals, natural or alopathic.