The cipher suites are controlled by the JSch libraries that are used by ApacheCamel. You can override the default list of libraries by using the appropriate java option found on their page here.
QIE automatically adds the older SHA1 cipher suites into the library, so if you want to prevent the QIE application from adding the old SHA1 ciphers in, use the java option: -Dqie.enableCamelSFTPSha1CipherSuites=false. This will cause QIE to skip the process of updating the cipher suites with the SHA1 ciphers.
Any change to the cipher suites in JSch apply globally to the QIE environment for all SFTP endpoints, so overriding any of the options will happen for all SFTP endpoints.
Additional Camel FTP options can be found here: