You can probably use Expect to give the password to crypt(1) in a secure way. I'd recommend doing that rather than re-implementing crypt(1) in Perl, since it avoids duplication of code.

As others have mentioned, on many systems the encryption provided by crypt(1) is very weak, and will really only stop casual observers from seeing the information in it. For better security, use something like Crypt::Rijndael, although that won't be compatible with vi.