File the appeal and tell your story.
Trouble is, I don't see the accusation that you "refused to do the job" as being false.
You were told to pull weeds and you didn't pull them. That's "refusal" no matter how you spin it.
Common sense dictates that the first time your boss responded angrily to your questions should have been enough to tell you not to question him any further.
All you had to do was move a little dirt from around the root and cut the root just below the surface and fill in the hole.

