As unpopular as it sounds, I think they should stick with the "choices have consequences" same as if you were to spend your two crafting tokens on skills then decide you wanted different skills... you made your choice.
I think you should reroll your character (I would, and have, for similar, bad skill choices), it's not totally back to square one as any bags, boxes, weapons and gear can be passed to the new char.
Especially right now, this is early access not Release, they have repeatedly said there will be a wipe upon release.
I have been testing the game since the alpha phase. Before EA, there was an NPC named “The Scavenger” standing by the well in Availia. You could learn harvesting skills there, even without the prologue quest in your journal. The NPC was renamed for EA and the function is now missing. It should always be possible to learn harvesting even without the pre-quest. The quest “A Hastily Scrawled Letter” that you start from the inventory is only good for guiding you to the NPC and is not a part to learning the skills. Before the EA, it was possible and that's how it should be. I think it's a bug and needs to be fixed for the NPC Liko (Gathering Skills) in Sorhiryth and for the NPC Foreman Aldeus (Gathering Skills) in Availia. That's my opinion.
You'll be happy to hear that the Scavenger has found a home just a short distance away in the Tavern :)
However, you can only learn the Harvesting skills thru the starter quest that you got from the Letter.
While I disagree with you about it being a bug that that the game contains no mechanism to 'fix' the problem that a player threw away an item (that was in their inventory when they first logged in) without bothering to read and understand what it was, it happens that VR has decided to help with that. You should put in a ticket to Support and tell them your character's name and server
The text for the Quest Giving the Tokens clearly states
"I only have two tokens for you, and you will not be able to get more."
However, it is just the same simple "Delete Crafting Apprenticeship Token?" Yes/No prompt to delete it as if it were a Tattered Pelt or something.
This is EA and part of EA I believe is finding issues like this, that need attention, and this one indeed needs attention. Something this important should be much harder for a person to mess up. Instead of Yes/No maybe type into a box "I Do Not Want to Do Any Crafting" and then delete it... not being facetious here, seriously it should be something without any doubt what you are doing, and THEN the "Choices have consequences" should apply. Maybe for Release.
I agree with extra safeguards. Like VR recently made it impossible to sell to a vendor any item that is currently equipped on your character.
Chances are nothing will get changed along these lines until much later indevelopment, as VR intends to eventually hire a dedicated UI Dev to revamp ALL UI screens in the Game, and that's not scheduled to happen until MUCH closer to Release. But it's good to get ideas out there for it.