The great thing about democracies is that the President or the Prime Minister isn't important, not really.
As I understand it the leader of Iceland (president, PM, whatever) has no security and lives in a medium sized house in a nice neighborhood. The General Secretary of the UN only occasionally has a moderate size security detail. The Federation President is probably more like the General Secretary of the UN and less the President of a large country.
If the President isn't the "embodiment of the Federation" and is instead simply the current and very temporary leader of the governing body, then killing or wounding him wouldn't be seen as much of a profound act or political statement. He wouldn't really be in all that much danger, because he is little more than a faceless bureaucrat.
Many of the peoples of the Member Worlds might not even know who he is. How many people in Europe could name the current head of the EU without looking it up? Or the UN?
Why kill him?
Mr. Laser Beam wrote:
You get rid of a president or prime minister by having these things called ELECTIONS.
Occasional running them out of town, covered in tar and feathers, could only be a good thing for a free society.