I've been through ZF and haven't had a problem casting LBs with the poly on my paladin. My macros are quite simple.. my Lightning Bolt macro is:
/target Party1target
/cast Lightning Bolt

I always use my 'spread formation' to break /follow before running my tank into battle, so I haven't had a problem with LOS. However, the macro works fine when my tank (Party1) has an enemy target even while polymorphed.