You're right that this might have been something simple, like amoeba, but what I mostly think of when I say "failure to thrive" is some internal abnormalities that just happens with all the selective breeding being done- & this one was apparently on the small side already which raises the odds of something else being off.
I do agree that a necropsy is always a good idea if your budget can handle it, & most especially to contribute to the bigger picture of knowing what went wrong, & protecting any other snakes in the vicinity in case it's something contagious, but in this case I think it's more likely the combination of an at-risk hatchling & perhaps waiting too long for feeding intervention.
For anyone intending to breed & sell snakes, for sure a necropsy should be done. My impression though is that the OP is more of a pet-keeper only, but I shouldn't assume. My bad.
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