The documentation says:
For each FTS virtual table in a database, three to five real (non-virtual) tables are created to store the underlying data. These real tables are called "shadow tables". The real tables are named "%_content", "%_segdir", "%_segments", "%_stat", and "%_docsize", where "%" is replaced by the name of the FTS virtual table.
So to get rid of that table, drop the shadow tables:
DROP TABLE tablename_content;
DROP TABLE tablename_segdir;
DROP TABLE tablename_segments;
DROP TABLE tablename_stat;
DROP TABLE tablename_docsize;
And then use the (very dangerous) PRAGMA writable_schema to remove the remaining information about this table from the system table:
PRAGMA writable_schema = ON;
DELETE FROM sqlite_master WHERE type = 'table' AND name = 'tablename';
SQLite caches schema information, so then you need to close and re-open the database.