I don't think we can look for 'guarantees' here when it comes to security, but we can imagine ways to improve on it, and to my mind having an extra person in the cockpit is better than none if a rogue pilot wants to bring down the plane.
Many have brought up EgyptAir 990 as an instance to prove the following sentiment: "well, if a pilot wants to bring down the plane, nothing and no one can stop him, even if another pilot is strapped in next to him." However, this leaves out the important detail in this case that the captain was not next to the f/o when the latter made decisive inputs for a CFIT. In fact, the capt was in the lav at the time. He returned disoriented/confused by the sudden descent and never seemed to realize that the other pilot was deliberately trying to bring down the plane (asking the f/o to pull with him (FDR suggests he wasn't, but the capt was seemingly unaware...I'm also aware that the Egyptian aviation authority disagrees with NTSB on the cause). Had he known of the f/o's intent, or had someone else in the FD seen him act suspiciously to initiate descent, he and others might have overpowered him and saved lives (as they did in the case of JAL 350).
Onboard battles don't guarantee a perfect outcome, but it seems to me physical force has a better chance of saving lives than nothing at all when it comes to a rogue pilot.