Unfortunately, I don't think it is going to be as simple as just removing the patch that changes VERSION to the SQLCipher version. Some places need the SQLite version and other places need the SQLCipher version. Probably the way to do this is make a SQLCIPHER_VERSION file, then edit configure.ac, tool/mksqlite3h.tcl, and src/sqlite3.h to use the appropriate versions.
Feel free to NMU this, or join as a maintainer :) I won't have time to test this in the near future.
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