An addition to the story of the Maghami - Shahar game in Corsica, which the Iranian GM (Maghami forfeited rather than play an Israeli, is found in the following chessvibe analysis, which I encourage all to read. It turns out that Maghami played all other Jewish players and even openly declared he had nothing personal against Israeli players (an act of courage on his part), but that he had no choice but not to play. Often, such excuses -- "I have nothing personal against Jews, but..." -- are just antisemitism in a flimsy disguise (much like "I have nothing against blacks, but...", etc.). In Maghami's case, however, knowing the character of the Iranian regime, it is clear he really did have no choice but not to play and really has no personal animus against Jews or even Israelis. This is not an uncommon situation: as Geurt Gijssen notes (quoted in the chessvibe article), usually such restrictions on playing come from the governments involved, not from the players.
Again, there is antisemitism here, but it is (as noted in the chessvibe column) it is usually by the governments, not by the players. It is a no-win situation, both for the players and for FIDE. If FIDE keeps the pairing and forces players to forfeit, they are punished through no fault of their own. If FIDE changes the pairings, one is encouraging such behavior (by the governments, not the players) and undermines FIDE's motto of Gens Una Sumus. My own view is that FIDE should never allow such re-pairings. If a country wishes to boycott another country, it should know it is violating FIDE's motto and that there should be consequences to this action. (Then again, perhaps it actually enhances FIDE's motto, which means in Latin "we are one family". Everybody knows of families where siblings hate each other's guts and won't talk to each other...)
It is true, of course, that not all political boycotts are morally equal. It is one thing for two countries in war to refuse to play each other, as sometimes happens. It is quite another thing to boycott Israel because one refuses to recognize its existence and as part of a plan to wipe it off the face of the Earth, as Iran's government does. However, it should not be FIDE's role to be a moral arbiter and declare which country is good and which country is bad. Quite apart from the very real risk of such "moral" declarations by FIDE bureaucrats becoming just another political tool, the simple fact is that FIDE exists, as Edward Winter pointed out in C. N. 1712, 'to organize chess, not court-martials against those with objectionable opinions'. Certainly boycotting, say, Nazi Germany in 1939 was justifiable; but it would be petty and unmanly for those who did it to demand that, since their boycott is morally right, they should not suffer the forfeit of a chess game as a consequence.