I have just come across the same problem raised in the thread "Library dependencies & make install" on the automake lists in January this year (<http://mail.gnu.org/archive/html/automake/2004-01/msg00145.html>) in a reasonably large project.
The last message in the thread from Alexandre Duret-Lutz suggests: "Another idea is to split the installation procedure in two steps: copy all libraries, and once it is done relink all libraries. Would that work? If so, we need a way to tell libtool to copy libraries without relinking."
I think the answer is yes, that would work. Are there any prospects of this being addressed?
Thanks, Fred
