Hertzberg writes of that passage:
By the time that long-obscure, lately apposite sentence became part of the Constitution, on July 9, 1868, the insurrection that occasioned it had been thoroughly, and bloodily, suppressed. Throughout the Civil War and afterward, Republicans in Congress had enacted some of the most forward-looking legislation in American history: a national currency, the Homestead Act, a transcontinental railroad, support for higher education, the definitive abolition of slavery—all thanks to the extended absence of delegations from the self-styled Confederate states. Now that era was about to end.
The party of Lincoln, grand but not yet old, feared the mischief that Southern senators and representatives might get up to when their states were readmitted to the Union. The Republicans’ foremost worry was that Congress might somehow be induced to cut funds for Union pensioners or pay off lenders who had gambled on a Confederate victory.