I think you can use "CHECK" for that:
CREATE TABLE IF NOT EXISTS "tag_parents" (
"id" integer NOT NULL PRIMARY KEY AUTOINCREMENT,
"from_tag_id" integer NOT NULL REFERENCES "tag" ("id") DEFERRABLE INITIALLY DEFERRED,
"to_tag_id" integer NOT NULL REFERENCES "tag" ("id") DEFERRABLE INITIALLY DEFERRED CHECK(from_tag_id <> to_tag_id)
);