You can save the SQL result to a file instead of it being printed to the standard output.
sqlcipher app.db
# Provide the key
sqlite> PRAGMA key = 'your_key_here'
# Save the result to the output file named result
sqlite> .out result
# Run the query. Notice that result isn't printed to the standard output
sqlite> select * from users;
# Display result to standard output if you want
sqlite> .out stdout