We are building an application which partially interacts with other system. We are pulling some data from the other system which is returned as RTF document. But we have to
Itext is abandoning RTF according to this post. One good solution I have used is JODCoverter Library. It leverages OpenOffice and I was able to convert several thousand RTF documents to PDF in the past.
Consider using a real word processor to generate the PDF. One posibility could be OpenOffice which has an API for this kind of problems - http://api.openoffice.org/ - which I would look into in your situation.
PDF's can be protected later using other open source software.