This brings the supposition that anyone deserves to be assassinated. For the purposes of discussion here, lets assume that it is morally right to assassinate a person if said assassination would serve to save a significant population of innocent individuals.
Notice all the little caveats there. What is significant? What does innocent mean? Is this the best working reference to go with? I don't know...but let's assume it is okay for our purposes here and get on with it.
Under this definition (or even one more liberal) Lumumba did not "deserve" to be assassinated. Though his political actions resulted in a bloody civil war and military coup (during which many people died) it was not his intention for these things to happen. In short, he had no intent to harm anyone through his actions.
He was not popular among Western powers because his actions destabilized his country, but more-so was his way of solving the problem. When the Western powers would not help him to suppress the rebellion in Katanga (largely instigated by outside forces that had mining interests in the region) Lumumba sought help from the Soviet Union. With their assistance, Lumumba attempted to invade the renegade province (a move that ultimately failed.) After this he was hunted by rebel forces and eventually both deposed and arrested.
Nobody knew exactly what to do with him, so the issue was decided when his opponents (and there is some evidence that the Belgians and Americans were complacent in this) drove him out in the middle of nowhere and executed him, thus solving the problem.
So, as you can see, Lumumba did not deserve execution. He was not a Hitler, or a Stalin, or a Pol Pot. He was just a man who fumbled the ball when trying to unite his fractured country. You can find a picture of the man himself here.
I think you can't answer this questions without asking first whether anyone deserves to be assassinated. It seems unlikely to me that there are very many figures in history who were so heinous that they deserved to be assassinated. Hitler, Stalin, people like that, sure, but Lumumba?
The main reason I don't think Lumumba deserved assassination is because it's not as if he was fighting for evil against good. As I understand it, the main reason he was killed is that his existence was inconvenient and perhaps dangerous for the fledgling government of Mobutu Sese Seko.
The years since Lumumba's death show us that Mobutu's time in power was not wonderful for Congo/Zaire.
So, if Lumumba was not personally responsible for great evil, and if the government that was behind his death was not much good either, it's hard for me to see why his death was deserved.