Just replacing the DLL isn't going to work because the API is slightly different. For example, how would DBD::SQLite know how to send the key to the dll? I'd think your best bet if you know C and perl would be to look at the installation package and see how hard it might be to add sqlcipher to the package. I'm guessing it would be fairly straightforward, but you'll have to spend some time to figure out how the module builds, build some test cases and such.
Failing that, you could offer to pay the maintainer to do the integration for you, or pay someone to create a patch for you.
When your only tool is a hammer, all problems look like your thumb.
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