It is indeed ambiguous, open to multiple possible syntax trees. Syntactic ambiguity is inevitable when there's many modifiers. The best you can do to clarify it is put a comma or rephrase it.
It is the piece, not the whole pizza, that is small:
- "작은, 피자 한 조각"
- "작은, 피자 조각 하나"
- "피자의 작은 조각 하나"
It is the whole pizza, that is small:
- "작은 피자의 한 조각"
- "작은 피자의 조각 하나"
Still, it's tricky to get rid of the ambiguity. Avoid such a construction whenever possible.