I managed to find a workaround. Thought i should share it with those who are faced with a similar issue.
I found that a bug report had been placed in the past with Apache Dev. However, they had said that they would not modify their logic because the servlet container spec requires it (even though isapi_redirector is only a connector and not a container). They said that there is no way for the isapi_redirector to differentiate between /foo/WEB-INF when foo is a context and when foo is just a sub-directory of the ROOT web application. So, the general consensus was to err on the side of safety and risk blocking a few requests that are valid.
However, this causes a serious issue for those using NetBeans JSF Visual Web Projects. Hence, I created my own flavour of isapi_redirector by modifying the code such that this check is not performed and leaving the onus of checking on Tomcat.
For those who are interested, the simplest way to go about this would be to force the function uri_is_web_inf (in jk_isapi_plugin.c) to always returns FALSE.
Just a little background on the issue for the sake of clarity:
Hence, my solution was to modify the isapi_redirector such that these requests were no longer blocked.