That's what a bill of rights is for. Any system of government that prevents governing is garbage.
It's not meant to prevent governing, it's meant to ensure that any legislation has the approval of the people at large and the states. If the Senate and House are controlled by different parties it means that they need to compromise in order to pass legislation. The United States is a union of states, it's a federation, it isn't simply a big group of 300 million people, and states rights is a value the people who created the constitution wanted.
If you don't have those same values that's fine. Canada also is a federal system, and we also have a Senate based on regional/provincial representation, but our Senate is much less democratic so by convention it defers to the will of the House because it's elected.