When using JAX-WS 2.1 and JAXB 2.1 with JDK 6, im faced with lot of issues.
To use JAX-WS 2.1 with JDK 6, newer versions of API jars (JAX-WS 2.1 and JAXB 2.1 API jars) need to be in bootclasspath before rt.jar.The only way to achieve this would be by endorsing
To do this you can use Java endorsed mechanism to override whats in Java platform. See http://java.sun.com/j2se/1.5.0/docs/guide/standards/.

As in my case doing so can have unintended consequences on other applications or other areas of the server, so it bares some risk.
Hence could please advice if there is an alternative to the above query without having to add an endorsed folder in my tomcat directory.

We've gone through the same thing, and that's indeed the way to go. VERY carefully handle the endorsing, and TEST, TEST, and test some more.