There might be some products which are capable of doing this, but I've written similar proxy myself where I wanted to serve local contents rather than remote for some uri's.
Here is a modification of my code written in python. It is based on the twisted library, so you might want to get it from here.
It will match for URL's with the netloc part equal to "security.stackexchange.com" and replace it with "www.xkcd.org".
I hope you are familiar with python, so you can add more functionality in this code. It should be easy to add logging, dynamically rewrite uri's and such.
Also, if you want to modify content in-transit from the malware and the C&C, take a look at my contribution for a content rewriting proxy: http://stackoverflow.com/questions/6491932/need-help-writing-a-twisted-proxy/6521024#6521024
from twisted.web import proxy, http
from twisted.internet import reactor
from urlparse import urlparse, urlunparse
fakeweb_netloc = "www.xkcd.org"
cc_netloc = "security.stackexchange.com"
res = urlparse(self.uri)
netloc = res.netloc
if netloc == cc_netloc:
netloc = fakeweb_netloc
self.uri = urlunparse((res.scheme, netloc, res.path, res.params, res.query, res.fragment))
requestFactory = ProxyRequest
protocol = MyProxy
if __name__ == "__main__":
factory = ProxyFactory()