Using a coin and freeing the soul are not synonymous, and must be described separately; you can use the coin once and not free the soul, because you only free the soul when you use all of the charges, which is not a part of the description of how you can use those charges. You can also free the soul without using any charges... so they must have independent paragraphs. Using all of the charges frees the soul: it says that in black and white, undeniably and unquestionably directly in the text. Freeing the soul is a good act: it also says that in black and white, undeniably and unarguably in the text.
Like ANY and EVERY magic item with limited charges, the section related to what happens when you spend all of its charges is a separate paragraph to the things you can do by using those charges. The section for Freeing the soul is in one part the paragraph that deals with what happens when you spend all of this magic item's charges, and in another it also contains ways of freeing that are not tied up with using the charges.
To be clear: I don't disagree that consuming the essence for healing definitely feels like you're doing something bad! It feels... wrong. However... formally speaking, as written, that's not how it works, and we either have to house rule it differently, or come up with a palatable explanation for what's actually happening when we do this. The explanation that by drawing energy from the soul you are less "breaking" the contract, and more "paying it out" to let the soul go early before it is totally obliterated is as near as I can think of for a palatable answer: I can image some poor being desperate to help her friends begging the coin she's carrying to lend her enough strength to do it, and in that exchange the soul giving its remainder and going free to its afterlife... I can wrangle that in my head, if I have to.
I'll quote again:
"A soul coin has 3 charges. A creature carrying the coin can use its action to expend 1 charge from a soul coin and use it to do one of the following:
Drain Life. [...] || Query. [...] "
"Freeing a Soul. Casting a spell that removes a curse on a soul coin frees the soul trapped within it, as does expending all of the coin’s charges."
The freeing a soul section is separate for multiple reasons, but primarily because they are distinct things, and also because the section deals with what happens when the charges are all used, and not with how you use the charges. Freeing the soul is not a function of using the coin - it's a result of using the coin. The section is telling you two things unrelated to how you can use the charges: what happens when the coin runs out of charges, and how to destroy the magic item without using its charges: that is why it is a separate paragraph... just like any other magic item with limited charges.
The meaning cannot get any more straight forward than this.
These are so evil that good characters can only bear to hold so many -- they are just worn down by hearing the screams of agony over time.
Wren, my poor little halfing bard with her negative constitution modifier and hoplessly idealistic, many-chance-giving heart can't even carry one - she'd be driven to the ground in a weeping, distressed mess, unable to move, just trying to hold onto a single coin, I think... she would never dream of taking its energy by force; the concept would horrify her... but she might ask it to help her, and and she'd defintely want to know who they were, and if there was anything she could do to help them...
