Regarding recent bugs I've had, I think it is a good idea.
A new Lintian rule could state "/etc/ld.so.conf.d/* must be prioritized" (in addition to http://lintian.debian.org/tags/package-modifies-ld.so-search-path.html and http://lintian.debian.org/tags/maintainer-script-modifies-ld-so-conf.html)
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