98% of criminal defendants are actually guilty, and are just seeking the best deal possible. Prosecutors are strongly disincentivized to prosecute cases without evidence because they get demoted or fired if their win ratio (including pleas) drops below 90%.

Public defenders don't advise their clients to take pleas in the absence of any evidence tying them to the crime, as claimed in the OP.

if nothing else, the 6-7 figure cost of defending oneself in court is incentive enough to take a plea.

This is false, unless you're convicted of murder and you choose the most expensive lawyers, and you proceed to trial, meaning that there was sufficient actual evidence of guilt that a prosecutor would risk their record and that a judge would commit the time and resources of his court to have a trial. Pre-trial costs for non-violent felonies are in the 4-low 5 figures. Violent felonies top out in the mid-5 figures. You don't see 6 figure costs outside of murder cases, and 7 figure costs all involve extremely wealthy defendants.

The financial cost of pleading guilty is 10x-100x the cost of defending oneself in court. If, as the OP claimed, his cousin was innocent, no defense attorney (public defender or otherwise) would have recommended he plead guilty, because based on what the OP said, there was insufficient evidence for the case to even make it to the preliminary hearing. In many states, the law enforcement agency at issue would have also paid his attorneys' fees.