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There is a rewrite, librasterlite2, available at https://www.gaia-gis.it/fossil/librasterlite2/index , which is "intended to completely replace the superseded librasterlite".
PyQGIS is the standard way to work with/automate QGIS processes and get it to do what you want it to do. Just call a PyQGIS script from your project. http://docs.qgis.org/testing/en/docs/pyqgis_developer_cookbook/
The solution was to use a kdtree instead of rtree. I used nanoflann. It runs about 20x faster.
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