Can someone suggest is there any other possible way to signing the XML message other than using MIME/SMIME Encoder & decoder in pipeline?
I am not sure whether we can use AS2 protocol for signing XML message and FTPing the message.
AS2 is not supported on FTP, only on HTTP & HTTPS.
Using the MIME/SMIME pipeline component would be your best option. See How to Configure the MIME/SMIME Decoder Pipeline Component and Essential Guide to Certificates, Encryption, and Signatures
Both the FTP adapter and the MIME/SMIME pipeline component need to run on a 32bit host.
Running the FTP adapter, POP3 adapter, and MIME Decoder on 64-bit host instances is not supported"