Barker's comments come after Wits confirmed they had sold their Absa Premiership status to Tshakhuma Tsha Madzivhandila (TTM).
"What happened (at Wits) is disappointing but there are always two sides to a story," Barker was quoted by Isolezwe.
"We need to thank Wits for their contribution to football in the country. Their development structures is world-class. I remember when I got there I was surprised by how well organised their development structure were."
Former Clever Boys boss Raymond Hack said they would still continue developing players after selling their status to the Limpopo outfit.
Hack said they only sold the certificate that permits them to play in the top tier but they would continue with their junior teams and development academy as the Wits brand would not be completely lost to football.
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