They had no choice - they were losing the case.
That's because those fools were to shortsighted, if they had let Milosevic win the case it would have legitimized the World Court by stating that you can be found innocent and let go.
Now, with them killing Milosevic, they have destroyed any legitimacy they may have had by them stating that if they cannot find a person guilty, they will just kill them before the trial ends.
Milosevic would have probably died within ten years anyway and he would have died in obscurity, all but forgotten, but now he is martyred and will probably be remembered for a lot longer.
Along with that, people now can use Milosevic's death as a justification to disband the world court in that anyone charged by the world court can now state that they will not get a fair trial and if they cannot be found guilty, they will be killed by the world court before the trial ends.