SkekSo's whole thing is knowing how to keep a tribe of socipathic hedonistic birdigators in check. While arrogant and corrupt, the Emperor seized and kept power because he knows what motivates his fellow skeksis.
So we have to look at two things. SkekTek is more independent than any other Skeksis. They all have their own interests and specialties, but SkekTek has his own lab, his own workforce, and most importantly controls something the Emperor does not fully understand. The Emperor uses SkekTek's skills as a club to keep his Skeksis from revolting when the crystal fails, he relies on him for, well, everything.
Of COURSE he's cruel, and you have to consider if that isn't what he's determined is exactly what's needed to keep the Scientist in line and from becoming the only real threat to his rule.