You have struck upon a very significant problem. In real life it is something that intentional communities often struggle with, wanting consensus but inability to reach it. Generally how I had seen it most frequently seen it dealt with in a way that still holds to principle of total consensus is that after talking out the problem and listening for legitimate concerns that can be addressed if a contrarian/bad faith element exists then it is made incumbent on them to propose an alternative. Meaning instead of the majority stressing themselves out and the minority extorting its leverage the table is flipped. The hold outs need to forward their own alternative or modified proposal and win the consensus of the others. It prevents them from sitting on their laurels and gumming up everyone else's vision. If they can hammer out something that does speak to the community after a time possible going back to be amended on the suggestions of the majority. But if they cannot produce an alternative proposal or cannot get the majority to agree within a certain time frame then there veto is overturned.

Not staying this might be a perfect method or there aren't better ones out there but this is a common practical one that allows dissenters to be heard and a chance to inject what is important to them but doesn't hold the majority hostage to few who might be irrational, selfish or contrarian.