Sion lives with pain. It is his strength. Nihilus' power comes from desperation and hunger. It would be his undoing. Sion's will would keep him alive, no matter the odds. I don't believe Nihilus could successfully cow Sion like the exile and Kreia could.
And as for him freezing you, it's probably because you didn't use the nifty force immunity power, or had the crappy saving throws of a Jedi Master/Sith Lord. Those two have the worst saves in the game. But I can't say. He never froze me. After my first hit he was too busy trying to suck my life out to heal himself. And since he couldn't...
But I will give Nihilus credit where it is deserved. He -was- keeping the ship, the slaves, and much more under his command while fighting three opponents (even if you could argue Canderous was a flea next to a Sith lord, in mixed company he was fine support).
I'm a bit divided. One thing I will say, however... Sion was considered one of the greatest Sith assassins in sith history. His specialty was more or less a saber to the back. Nihilus was hunger given personification. The battle would be circumstantial. On the bridge of the Ravager? Sion. Elsewhere... Perhaps Nihilus. Who can tell?