From the perspective of counterparty and the overall bitcoin community,

• The criticism is not against counterparty, but just One Flaw in the system
• There was zero consultation on the design with the wider community before the "on" switch was flipped
• This flaw --network-critical database used for raw data storage-- was well known before Counterparty began life. You could have avoided this problem with communication.
• Existing designs are known to be less abusive to the network, and do not store data in that key database

It is perfectly possible to run counterparty without this flaw.