Rose,

The Vicksburg paroles did not mean that a man would never again take up arms against the US. They said that the man signing the parole would "not take up arms again...until duly exchanged by the proper authorities." After the surrender, they were to report to parole camps where they would await the exchange process. After their release, many went home first, and others went home after furloughs were issued at the camps. Large numbers returned to their units, but many did not. Some joined other units, some stayed home.

Here is a very good description of the process and the aftermath:

http://www.history-sites.com/cgi-bin/bbs62x/alcwmb/arch_config.pl?md=read;id=4894

Do you know that your ancestor's pension application was approved? That may shed some light on whether or not state authorities felt that he had served honorably and proven his loyalty.