Unless you're prepared to do a lot of low-level coding and/or high-level hair-pulling, my suspicion is that WebRTC isn't quite ready for a scenario like this one quite yet. There are some folks who have managed to get it working with some servers like Asterisk, and there's supposedly a general purpose SIP client available here: https://code.google.com/p/sipml5/. But from what I hear hanging out on the WebRTC mailing list, folks are having a fair bit of trouble with these integration scenarios. There's certainly nothing that just works out-of-the-box. Lync supports SDP and SIP, but I expect that you'd need to spend a lot of time figuring out how you need to transform the SDP that WebRTC generates before it ever gets to the Lync server.
[Edit 1/28/2013] - Beyond the issues above, the real problem maybe with the codecs that are supported by each platform. Currently, I believe that the only codec supported by WebRTC is Google's VP8, which doesn't appear to be supported natively by Lync. So you'd need a realtime gateway/transcoder sitting between them, translating between H.264 (or whatever protocol Microsoft Lync settles on) and VP8. Assuming you can find a gateway to do that - they may very well exist - I can't imagine it's going to scale very well.