Who better to answer this than Sentinel himself?
Sentinel: Commencing transport.
Optimus: Stop! No, no, no Sentinel!
Sentinel: Forgive me.
Optimus: Autobots, retreat. Why Sentinel, why?
Sentinel: For Cybertron. For our home. What war destroyed, we can rebuild. But only if we join with the Decepticons.
Optimus: No, it's not the only way. This is our home. We must defend the humans.
Sentinel: So lost you are, Optimus. On Cybertron we were Gods. And here they call us machines. Let the humans serve us. Or perish. You're lucky I didn't kill you. In time, you'll see.
Optimus: It's not over.
Dark of the Moon script
Sentinel gives an implication as to why he spared Optimus. Sentinel was being treated like a "lower-being" on Earth, and being a haughty individual (he was a Prime), didn't like this as well. He wanted to be treated like a God. He wanted Optimus to watch the Cybertronians take over Earth, and subsequently join them in ruling Earth, hence he let Optimus live.