Is this a genuine concern of just FUD?
That is FUD. There are many ways to store Counterparty data in the blockchain. It's not leaving any time soon, no worries. Everything is stored in the blockchain, and cannot be changed or manipulated without manipulating the blockchain itself.
That's right. It's pretty much impossible to prevent Counterparty from using Bitcoin, because of the many ways in which Counterparty can store data in the blockchain.
BTC has strong incentives to prevent/penalize "parasitic" data in its un-prunable blockchain.
OTOH, Cryptonite welcomes messages being passed through its fast and light mini-blockchain:
Cryptonite has superior support for micro-transactions because we don't have to worry about keeping any so called "dust" in the blockchain forever. Since blockchain bloat is not a problem, blocks can be larger and we can encourage the use of custom transaction messages.
Like micro-transactions, although possible, the Bitcoin community tends to discourage the storage of text messages in the blockchain because they must be stored forever. The early versions of the bitcoin-qt GUI included a feature for including a custom text message with your transaction but it has since been removed from the GUI in order to slow down blockchain bloat. Including a custom message with a transaction is a very common and useful feature that can play an important role in many merchant scenarios, so it's clearly important for any currency to support such a common and useful feature.
The scalable nature of the mini-blockchain scheme relieves us from the concern of blockchain bloat and we can have full support for transaction messages for the same reason we can support micro-transactions: all the transactions containing the messages can be forgotten by the network after some relatively short period of time. Cryptonite has native support for attaching custom messages to transactions, since we don't use script the message field is embedded into the structure of the transaction, meaning you cannot have a different message for each output, only one message per transaction.
Cryptonite is based on BTC, so modifying/extending XCP compatibility to use it isn't much of a stretch.