The reader is left to harmonize these seemingly disparate texts produced by one and the same author.
At least four options present themselves for such a harmonization:
First, one might hypothesize that Paine changed his views between 1776 and 1797. Reasonable men do, after all, redesign their schemes based on experience and reflection.
Second, the reader might conjecture that Paine was tailoring his proposals to their audiences. Common Sense was written for the United States, while Agrarian Justice was written for France, with a possible sidelong glance at England. Perhaps Paine reckoned that the United States was fit for a radical degree of liberty, while the older nations of Europe and Britain were ready only for a more modest amount of freedom.
Third, one might suppose that Paine was capable of holding inconsistent ideas. More than one author has entertained mutually exclusive propositions, and either not been aware of the internal contradiction, or not cared about it.
Fourth, the reader might understand Paine as making a terribly nuanced argument, which would depend on a tortured reading of the text of Agrarian Justice, namely, that the planned redistribution - Paine wants the landowners to pay a percentage of their harvests to a treasury which would dispense such funds to all who did not own land - would somehow be a private sector operation, and thus avoid the stigma which Paine attaches to government in Common Sense. While such a reading would make Paine the author of an attractive scheme, it is very challenging to read this scheme out of - or into - the text.
In addition to the four listed here, there may be other interpretive possibilities for understanding Thomas Paine. But the paradox which he presents will prevent him from being a simple mouthpiece for any political grouping.