The President is head of the Executive branch. It's his duty to enforce Congress's laws.
Pot is illegal at the federal level (aka Congressional law). It's against the law to possess, sell, etc. So unfortunately the President is legally required to prosecute this.
Now, given that, I am a bit disappointed this is happening. There are plenty of other more important things to prosecute more zealously. Especially given Obama's "bigger fish to fry" comment.