Dhaval,
Looks like I had a similar problem back in 2006 when working with BizTalk 2004…..
I had a customer that needed to receive messages that included the DTD DOCTYPE declaration so wrote a Send Pipeline component (see http://www.modhul.com/2006/12/28/add-doctype-declaration-component/ for source code) to add the DOCTYPE back into the message based on the MessageType (the message coming out of BizTalk did not include the DOCTYPE declaration).
You will need a similar Receive Pipeline decode component that removes the DOCTYPE as the message is received into BizTalk so it doesn’t break the Xml Disassembler – you could perform this with a simple RegEx replace for example.
HTH, Nick.