I don't know about Solaris 2.6, but I know that installing over top of the factory-installed perl in Solaris 8 (might've been Solaris 7) caused problems. (what they were, I don't particularly remember, as it's been a couple of years, and I learned from it, and never did it again).
So long as you install into /usr/local/bin, and do not replace the perl in /usr/bin, and do not set root's PATH with /usr/bin/local before /usr/bin, you'll be fine.
Users can then specify /usr/local/bin/perl or /usr/bin/perl as they want in their shebang lines. You will have to install whatever modules you may need all over again, and you should not have them use the same include paths (unless possibly if you have locally maintained pure perl libraries that you don't want to maintain in two places, you might share those, but for everything from CPAN, I'd install all over again).
I'm guessing though, if you're still running Solaris 2.6, you have other problems to worry about. (2GB file limit which could result in truncated backups, etc.) Depending on the exact situation, I might push the 'we need to upgrade', just to move off of Solaris 2.6, if that's what it would take to push the change.