I have personally seen big companies reject systems because they were written in Perl for this reason.
True. On the other hand I have also seen companies reject systems because they do not have access to the source. Depends on the client. Depends on the job.
Languages like Perl and Java running on a relatively high level VM are far easier to de-compile than something that compiles down to machine code. So, don't use them for projects when simple access to the source code is an issue. Any "compilers" or "obfu" generators that leave the VM code around are pretty trivial to get around.
Personally, I do the vast majority of my commercial work in areas where access to the source isn't an issue - indeed it is usually required.