Yep. Remember earlier in the season, Mrs. Petrelli taught Sylar how to absorb people's abilities though concentration instead of removing their brain and studying it. Elle was the first person he learned from without harming. He's only killing now, because that's just who he is.
I have a feeling when the time comes for the real Nathan to return, they'll pull out the oldest trick in the book to explain it...The end of Season 3 was one of Angela's dreams and didn't happen.
...But he told Mohinder that Maya's power was completely gone for good, which indicates that he does take the ability for all time, unless that is completely selective, depending on his victim. He might decide who loses their powers for good and who is powerless for only a period of time.