If you are actually scared about people calling your game racist based on whether your characters are white or black, then make them all blue blobs of translucence gel. Or better yet, make them constantly shifting colour and spending an equal amount of time in all parts of the visual spectrum.
Oh wait, better go with UV and IR at least a little, or someone might complain that you're excluding that too. To hell with it not being something you can actually display on a monitor,...
Blue blobs?? LOL. But also an interesting idea. Perhaps the character can use the aliens tech to take over other creatures on board, or control other avatars remotely.
If you have to ask these questions then you probably should not embark on such a thing.
There is nothing stereotypical about a black character in a game (or movie or book or whatever) being a slave. What could result in backlash is if you portray the character as an ugly, stupid, shallow, unreasonable, one dimensional, ignobal, undignified thug.
I'm surprised at some of the earlier responses who think that merely having a black main character who is a slave might be construed as racist. For someone to think that black folk would automatically react in such a way regardless of the quality of the final game character, might suggest that they think black folk are irrational and that such considerations would not be taken into account. How ironic.