On other platforms, this is solved by nspluginwrapper, which runs the plugin as a separate process and just sends events and screen contents between them. Given that most web browsers now do something similar for security and stability (so a plugin can't crash the browser and a security problem in the plugin is isolated), it's not likely to be a significant issue.
Unfortunately, Windows' security model is somewhat different to X's, and under Windows you can't just have two processes rendering into the same window without them being written quite carefully to cooperate with each other. Chrome is able to do this, but AIUI the method they use to make it work is (1) so complicated nobody else has even tried to make it work and (2) relies on a hack that fails if they try to have one of the processes as 64-bit and the other as 32-bit. AFAIK, Chrome is the only browser that runs NPAPI in a separate process under Windows.