>> I feel like there has to be an effort at all layers of government to solve this structural problem where a few homes can derail a democratic process.
What you describe is not a structural problem. On the contrary, it is precisely how a constitutional, rule-of-law system is meant to work.
Democracy does not mean pure majority rule. Our system is a constitutional democracy. Majorities make policy, but minority rights and legal limits constrain how they do it. Courts are there to enforce these limits even when a policy is popular.
Judicial review is part of the design. Reviewing legislative and administrative actions for legality is a built-in check and balance, not a veto by randos. The courts exist to ensure the other branches do not skip required steps or exceed their authorities.
More specifically, the legal concept of "standing" prevents this from being arbitrary. In most contexts, you cannot sue just because you dislike a decision. You must show concrete injury, such as living next to an affected area. That's why a "few households" can file: they're the ones with legally cognizable stakes.
Now, I will grant that in places like California with decades of existing laws, NIMBYs have done an excellent job figuring out exactly what buttons to press and what levers to pull to get their way. But this is not a flaw in the system. It just means that they have read all the manuals (because they are very strong incentivized, financially, to do so) and are now using it competently, even if it is self-serving and sometimes even in bad faith. But other locales have figured out the solutions to this problem. The article gives one such example: Austin, TX.