To my surprise, Werner Koch (author of gnupg) has jumped into the 'librfid' project by contributing his USB CCID low-end driver to it. Using this driver, it should be possible to use librfid directly on the reader, instead of going via OpenCT. There's nothing wrong with OpenCT, as it is the only way to support contact-based and contactless operation at the same time. However, for development and testing, most people don't really need that feature.
Unfortunately it only works theoretically, must be some minor difference in device initialization that causes breakage.