The game did feature a form of slavery with indentured servants from Europe, many of those ended up being literal slaves with no end to their contract once in the new World.
Regarding the issue of slavery, Colonization would have been criticized both ways: had they included it, they would have seen as condoning it. Removing it makes it seem like they did not care or are trying to hide it from History.
There's no good solution that will satisfy everyone.