How does dfinity protect against using many update calls to make canister run out of cycles?

Did you mean canister sandbox, not LLVM here?

LLVM is a toolchain for compiling program that the Rust compiler uses under the hood. I am pretty sure that the Internet Computer source code is compiled using standard Rust, which uses standard LLVM.
I never heard about a custom LLVM for Internet Computer. Forking LLVM to create some custom version of it would be a huge engineering effort and I don’t know what would be the benefit of it.

If you meant canister sandboxing, then there are public resources explaining it:

Canister sandboxing uses a common technique of process isolation with SELinux. If you have concrete technical questions about it, I’d be happy to answer.

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