There's really no indication that Thanos had anything to do with Loki replacing Odin. That's rather difficult to fit into the timeline of events. And giving the Aether to the Collector doesn't really help Thanos at all.For right now Thanos appears to be playing a chess game of sorts, but I do believe he helped Loki take out Odin and put Loki on the throne of Asgard at the end of The Dark World, I can't see Loki doing that on his own. Plus it was "Odin" who ordered the Aether to be given to the Collector.
What timeline? And it's highly unlikely that Loki took out Odin by himself if he could've he'd done it years ago he had to wait for Thor to on earth and Odin was in the Odinsleep when he took over Asgard in the first Thor movie. It's doubtful that Thanos knew where the stones but now that the Tesseract in on Asgard, the power gem in on Xandar and the Collector has the Aether he knows where they are. If the mind is in the sceptor and I think this is likely he knows where it is as well.
It's obviously not a fact, but my impression is that Loki and Odin switched places well before the final battle, so that Odin could go on his adventure with Thor, and then when we saw Loki die in the movie that that was Odin who died.
It was a Parent Trap.