I don't see the problem, or what compromises privacy exactly?
Say you have UTXO A1 and B1 of 0.001, (I've never used Coinjoin so i'm just assuming here.)
Now you put both A1 and B1 through Coinjoin, Now you have A2 and B2.
How would combining the outputs of A2 and B2 compromise the privacy of outputs A1 and B1?
You used CoinJoin to break exactly that chain right?
Put the balance of the change adresses all individually through coinjoin mixing sessions and then combine the outputs? That way the chain is broken, and due to them being linked only after the chain was broken, privacy isn't compromised?
If they're too low of an amount to be send to Coinjoin, i'm afraid it's just dust, and they should be frozen to prevent them from accidently being spent in the future when tx fees might be lower again.