In what way would checks and balances do that at all? The only branch that has any sort of leeway to pass unpopular policies is the Supreme Court, and setting budgetary constraints is far outside their purview.
Unfortunately the U.S. constitution was written with the, in hindsight, naive assumption that political parties could be avoided.
This just led to a system that has political parties but doesn’t really acknowledge their existence and therefore makes it difficult to regulate their behavior.