My (original, Mac OS 10.7.4) openssl was installed in /usr/bin, you can trace it by opening the terminal and executing "which openssl".
If this does not point to /usr/bin/openssl, you could probably try verifying that the "original" (most likely) openssl still exists in /usr/bin/openssl by executing "file /usr/bin/openssl". This should return something like the following:
/usr/bin/openssl: Mach-O universal binary with 2 architectures
/usr/bin/openssl (for architecture x86_64): Mach-O 64-bit executable x86_64
/usr/bin/openssl (for architecture i386): Mach-O executable i386
If your "which" command points to another location then /usr/bin, and the file command verifies that the original binary is still in place, you could probably try to verify your mobile provisioning files with that.
Instead of executing "openssl smime -in "path of mobile provision profile" -inform der -verify", execute it by calling the specific binary you want in the following manor: "/usr/bin/openssl smime -in "path of mobile provision profile" -inform der -verify"
If you want to go back to the old openssl binary permanently, you will have to remove the "new" openssl.
If you installed the new openssl in /usr/bin (eg, the original binary does not exist anymore), then you'll have to find some other way to install the original openssl.
Maybe you can link the tutorial / guide you followed to install your new openssl? This would help people here to determine what you actually did 😉