I know that there are many who will disagree with me on this matter, but even in this sad episode, Hakol LaTovah, it was all for the good. Here are some things to consider:
1) Before his capture Jonathan was a fairly assimilated Jew, far away from Torah and Mitzvot. During his jail stay, he became more observant, and was taken under the wings of one of the generation's greatest rabbis, Rabbi Mordechai Eliyahu zt"l. What started as a desecration of God's name has become a sanctification of His name.
2) By seeing the way the United States discriminated against Jonathan Pollard, American Jewry learned once again that Jew hatred exists at the highest levels of government. Pollard's suffering has come to teach Jews all over the world and especially in the United States that it's time to come home tho the land of Israel!
3) There is even a silver lining to the restrictive conditions of the parole. We can compare Pollard's redemption to the nation as a whole. The redemption of the Jewish People comes little by little. Why is this so? Because the transition from the darkness of the exile to the bright light of redemption would be hard to handle, if the redemption were to come all at once. Jonathan's gradual acquisition of freedom may actually be good for him in the same way.
Shabbat Shalom to Jonathan and Esther Pollard and to the entire Jewish People.