website a is referecing website b - how do I handle this on the ltm

The first thing I'd ask is if web2 has an external LTM/APM interface? If it doesn't, then it wouldn't matter that the URLs are internal and unreachable. If it does, then you may consider using the same iRule to rewrite links to web2 (to its corresponding external LTM/APM URL). Not sure what your iRule looks like, but this is usually a matter of rewriting HTTP redirect Location headers and (if necessary) applying a STREAM profile on HTTP response traffic to rewrite links in the payload.

An even easier option may be to simply use an APM portal configuration. All access to web1 and any internal references like web2 would be automatically rewritten to flow through the portal.