Beanstalk apparently set up what amounts to staking system for votes. More money == more votes. Have enough money? Well, then you have the majority of votes and can do whatever you want.
This is precisely how the system was designed to work. They just didn't foresee someone building up a large enough stake to amass the voting power needed to undermine the system. And that is simply a failure of imagination and goes to show how naive these folks were.
The way this works in the real world is you have a limited number of shares that give individuals some number of votes, and those shares change hands. In order to build up a large enough position to control a company, you have to convince existing owners to give up their stake or vote with you.
But if every dollar contributed to a "silo" creates a new vote, then yeah, you're basically saying: If you're rich enough you can take control of the project by simply amassing a large enough fortune in the project.
There's probably things they could've done to reduce the likelihood of an event like this--e.g. requiring supermajority or unanimous voting for certain types of changes, for example--but they didn't, so here we are. The system worked as intended.
And yes, I really mean "intended". They intended for people with more money to have more of a voice. And this is the (extremely obvious) consequence of that choice.