If she knows you're aware of the missing pills,....if she knows you realize she's the only one who had access to those meds (if that is indeed the case),....and if she knows you're taking this issue seriously enough to file a claim with the police (it's a federal offense),....that may be,....just may be,...enough to at least stop her in her tracks.
IMPORTANT INFO: I would get an official police report and fill it out and show her a COPY of it, (NOT the original,....to be shown the original would leave room for potential doubt as to if you're even serious about really filing, or if you ever even will! Where-as a COPY strongly implies the police have the original).
You need never convey whether the police do or do not have the original. Keep that to yourself, and let her wonder! Whether you decide to actually file it or not is another matter you and your wife can discuss, but most people will feel more motivated by fear in seeing a copy of a police report with their name on it, especially for something like this which would be several different charges, among them felony and larceny of a controlled substance.
Even if she snaps back and defensively retorts that you "can't prove it," --then she just confessed. THAT kind of comment in itself is an admission on her part and a sign of fear. That will give you the info.
And I can't stress enough, many of us have learned the hard way,....and especially after something of this magnitude: You simply must put those meds in a secure, fire-proof, lock-box. To NOT do it is inviting theft again, and sending the message YOU are not taking this seriously.
To NOT secure the meds in this way is an admission that you're blustering and making idle threats, that you probably didn't file a police report, that you probably never will, and that you're "open for business" so to speak. What you DON'T do can speak volumes.
EDIT: I just noticed the OP hasn't returned to read or reply to our thoughts, many of which are passionately written. :(