NAP. She threatened him and he had no recourse to go to the police due to the drug war. Also, she was putting his friend and business associate in danger. Her death very likely saved Jesse's life.
I see your point - it's totally valid, but I feel like she was so motivated by money and the prospect of getting away that Walter could have found an option other than killing her.
Walter proves throughout the show that he's pretty darn clever when it comes to manipulating people - dude has got the skills to make stuff happen. Killing Jesse's girl was an easy way out of a situation that I'm pretty sure his character was clever enough to deal with without destroying a sad and tortured life.
Sure, she threatened him - threatening is not doing...killing is something you can't take back. He could have moved her passed-out-smack-filled-body back to her place and called her father or dropped an anonymous call to the cops - someone clever could come up with a better plan that this - but these are some options.