I finished season six

1. Samuel might have been trying to get Mary back (and I do understand him trying to save his only child), but he was also willing to work with Crowley - the King of Hell - and betray his grandchildren to do so. Also, as I remember, Samuel was possessed by the worm thing Eve had created at the time.

2. By the time Cas killed Balthazar, Cas had been working with Crowley for ages, trying to find and open Purgatory. The Winchesters had found out about this and told him not to. Cas basically said that if they weren't with him, they were against him and were his enemies. Then when Balthazar was also working with the Winchesters and trying to stop the opening of Purgatory, Balthazar was also Cas' enemy.

I haven't watched S6 for a while, but I'm pretty sure that both these explanations are true.