Say I have a smart contract the preforms a specific function and is used in a decryption process off-chain. Would it be possible for Molly to download the entire contract and run it on their own local node, thereby brute-forcing the decryption element of the smart contract. She would do this as she is not limited by the slower block times of the public chain.
Nope, you'll be good. Assuming they know the address, they'll just be able to run the public functions and see the public variables. If you don't even want them to be able to see the functions, you can even make that private as documented here: http://solidity.readthedocs.io/en/develop/contracts.html#visibility-and-getters
If someone brute force breaks the ethereum encryption mechanisms then the whole system is fubar, so just keep your variables private and use keys to store data and you'll be good to go.