I would like a perl module (even if it's just a wrapper) to identify
what pronouns refer to (entity recognition). Eg:

The car belongs to Billy because he's the guy who painted it. 

It would work out that "he" refers to Billy, "it" refers to the car
and perhaps "the guy" referring to Billy too.

I'm aware there's a few alternatives available for this in Java like
GATE, JavaRAP but I need something I can control from my perl code.

perhaps the lingua::LinkParser can do it for you? I can't see what
link types are defined in lingua::LinkParser::Defintions, but if a
pronoun linkage is defined, perhaps this will work.

Worst case, you can use Inline::Java 
http://search.cpan.org/~patl/Inline-Java-0.51/Java.pod
It is very straightfoward.

oops, forgot lingua link:
http://search.cpan.org/src/DBRIAN/Lingua-LinkParser-1.09/README

Interesting module. At first look it doesn't seem to want to help me here. 

It outputs the same for 
The car belongs to Billy because he's the guy who painted it. 
and
The car belongs to Billy because John's the guy who painted it. 

But I'll look into it further.