Richard Boswell has published an article called "Crafting an Amnesty with Traditional Tools: Registration and Cancellation," 47 Harv. J. Legis. 175 (Winter 2010). In this article, Richard focuses on the best way to structure an amnesty program rather than on justifications for one.
The article argues that four overarching principles should govern an amnesty program: (1) the program should be rooted in preserving family unity, meeting needs for work skills, and fostering humanitarian values; (2) the program should in part aim to ameliorate unnecessary hardship to the individual applicant as well as to the community of which he has become a part; (3) the statutory scheme should be as simple as possible to minimize multiple or conflicting interpretations; and (4) ease and comprehensibility of administration.
Here's the link: http://ssrn.com/abstract=1563627