Why Did God Take Sam's Soul?

Theory 1: He Needs Sam to Do Bad Things

Perhaps God kept Sam's soul because He knew that, in order to stop Samuel and the plot to kill the Alphas, Sam would have to do things and make sacrifices he wouldn't be willing to make unless his soul was removed.

Theory 2: Sam's Soul is Corrupted

Like a computer infected with a virus, maybe Sam's soul was corrupted by Lucifer's presence, so the only way to bring back Sam without bringing back Lucifer was to take his soul.

Theory 3: Sam is an Alpha

This is my favorite of the three theories. If Sam is an Alpha, then maybe keeping his soul was a way of ensuring that Samuel wouldn't be able to collect one of the Alphas. Sam was one of the special children and he was integral in Azazel's plans, so it would make sense that Sam, and possibly even Dean as well, are both Alphas.

Where is Sam's Soul?

Finally, the last part of my theory is about where Sam's soul is, which seems obvious: It's in Dean's amulet necklace. Missing since Dean threw it away in season 5, the amulet is the perfect location for Sam's soul, though perhaps I'm being biased by the film Men in Black, where the miniature galaxy everyone was looking for was actually in a cat's collar the entire time.

So what do you think? Is God a part of this and is Sam's soul missing for a good reason? Are Sam and Dean Alphas? Or is there a better explanation for everything?