Is it permissible for me to pay Zakat al-Fitr on my behalf in Morocco and on behalf of my wife in Egypt, or must it be paid for both of us in one place (either Morocco or Egypt)?

The basic principle is that Zakat should only be paid to its rightful recipients in the country where it became due. Since you are obligated to pay Zakat al-Fitr for yourself and your wife, you should pay it for yourself in Morocco and for your wife in Egypt, as the determining factor for Zakat al-Fitr is the country of the person on whose behalf it is paid.