Starting with Lincoln, and continuing with Johnson, there were a string of presidential pardons. All had conditions, and Maury was not then eligible based on these conditions. However, on Christmas Day, 1868, Johnson finally pardoned all former confederates unconditionally. Maury had lived abroad until this point, but came home after this. The last southern state readmitted to the Union was Georgia in July of 1870.

All Section 3 of the 14th Amendment did was prohibit former confederates from holding public office, unless Congress voted otherwise by a 2/3 majority. It "rehabilitated" no one.

Maury was "restored" (pardoned) in 1868 (as were all confederates) but not eligible to hold public office. As it was, he took a position at Virginia Military Institute.

He would then be "off the hook...so to speak," and the ship should then not have been renamed, according to your belief as just expressed.

Before he resigned his commission, and joined the rebellion, his naval accomplishments were respectable and notable. It could be (and has been) argued that the several things named for him (not just this ship) honor those accomplishments. That certainly does leave aside his accomplishment of leaving the Navy and the Union, and of his several accomplishments while in Confederate service.

The post Civil War nation was divided between reconciliation and retribution, and the history shows a mix of both. And this history continues.