Is she leaving Elementary?

You may well be correct about Ophelia filling in whilst Lucy was on another project. But if you look at Lucy's history in IMDB there doesn't seem to be anything running mid 2014 onwards. Lots of voice work but I'm guessing that could be fitted around her Elementary schedule. Though there could be events in her private life or aborted projects or perhaps even some stage work that would fit your hypothesis. Alternatively, perhaps Ophelia's stint on the show was always intended to be a half-season story arc to bridge a kind of dramatic gap when Holms and Watson 'seperated'?
Personally I wasn't sure about the new character in the show at first but by the end of the 12 weeks I was sorry to see her go.
Finally, whilst I like Lucy Lui very much as an actress I'm not sure she in the bigger star. Yes she has a longer track record on American TV series and stared in a lot of B movies. But Johnny Lee Miller has quite a strong track record in film and TV plus his highly acclaimed stage work. I'd actually rate then as about equal which is one of the reasons the show works so well.

I would like to see her in a spin-off, perhaps as a vigilante who trains other abused women.