From a compliance perspective, organizations need to have a hardening standard derived from an authoritative source with solid engineering-based reasons of why we depart from any of the recommendations. Most organizations use the Center for Internet Security (CIS) Hardening Benchmarks because that choice is easy to defend. The CIS benchmarks reflect industry consensus around hardening best practices and therefore adopting the benchmarks is an example of due care.
A hardening standard is intended to be a shared, living document that evolves with threats and lessons learned by the organization via a change control process. To ensure consistency and follow DevOps principles, the application of the hardening standard should be scripted and managed via change control. It should also be audited to ensure that the expected configuration remains in place over time. I have found that Lynis (https://cisofy.com/lynis/), an open source tool is is a great way to audit a system for CIS benchmark compliance.
Obviously, there are multiple ways to script the implementation of the hardening guidance. Here is an example for Ubuntu 14 that simply modifies the weak, default security settings of the base OS as distributed - https://github.com/Resistor52/SampleLinuxScripts/blob/master/harden-UbuntuServer14.sh