The biblical system only works, if the entire society supports the judge's decisions. Submission means supporting the decisions of good judges.
We can strengthen the authority of excellent judges helping to them to implement decisions. For example, a good judge will sentence a convicted thief to pay restitution, but he will not be able to use physical force to obtain the restitution payment.
However, if the rest of society refuses to deal with the thief until his restitution is complete, he would have no choice but to comply with the judge's decision. Good judges will get their decision supported, because other members of society help implement them.
This also works to keep the judges honest. If they start making unjust decisions people will withdraw their support and they will lose their reputation.