Você precisa de aspas simples em torno do ! para impedir que a expansão do bash e \ escape do $ :
ssh root@$remote_machine " awk '/^#/ || "'!'"a[\ssh root@$remote_machine " awk '/^#/ || "'!'"a[\%pre%]++' /tmp/file > /tmp/file.new"
]++' /tmp/file > /tmp/file.new"
man bash explica por que tentar escapar do ! usando \ não funciona no seu caso:
Enclosing characters in double quotes preserves the literal value of all characters within the quotes, with the exception of $, ', \, and, when history expansion is enabled, !. The characters $ and ' retain their special meaning within double quotes. The backslash retains its special meaning only when followed by one of the following characters: $, ', ", \, or . A double quote may be quoted within double quotes by preceding it with a backslash. If enabled, history expansion will be performed unless an ! appearing in double quotes is escaped using a backslash. The backslash preceding the ! is not removed.
O caractere \ não será removido depois de escapar do ! . Isso explica o erro de sintaxe awk obtido.