In this wiki it is stated, that the Supreme Intelligence was replaced by the Kree Emperor, but was this officially confirmed? Just because there is an emperor it does not mean, that the Supreme Intelligence can't be still the ruler. For example the UK has a Queen, while it is acutally governed by a Prime Minister, so why should it be not similar with the Kree Empire? It would be possible, that the Kree Emperor is just the symbolic leader of the empire, while the Supreme Intelligence is the actual ruler.