Strike when he is asleep or unprotected, give him a concussion that wont trigger the failsafe. Make him sleep / unconscious forever , but also give him human needs so he dont die and failsafe gets triggered.
The failsafe activates whenever he's in danger, not necessarily when his life is threatened so I don't think that would work. Also, this is a very cheap shot, it's not a way to beat him, it's a way to just take him out when he can't defend himself.
I’ve proposed a scenario of mind controlling somebody like Kevin and then stabbing Ben through the heart, which would totally kill him.
Granted, the Omnitrix needs to be aware that Ben is in danger. How exactly this is determined is unknown, so things like viruses and other diseases, as well as say, continual doses of radiation could theoretically bypass the known failsafes.
A realistic way is having someone sneak in the plumber hq as a plumber and have blukic and driba make an omnitrix controlling device(as seen in an episode) and then it should be pretty simple. Though it would be hard, but still should be effective if it works.