How can I force MySQL to IGNORE ALL indexes?
It's absolutely not clear why you want this but you can use the hint USE INDEX () to tell the optimizer not to use any index. From MySQL docs: index hints


  It is syntactically valid to omit index_list for USE INDEX, which means “use no indexes.” Omitting index_list for FORCE INDEX or IGNORE INDEX is a syntax error. 


Your query becomes:

SELECT count(*) AS c, 
       substring_index(domain_name, '.', -1) AS tld
FROM domains_import 
       USE INDEX ()        -- use no indexes
GROUP BY tld
ORDER BY c DESC
LIMIT 100 ;




Side note: the complex expression:

SUBSTRING(domain_name, LENGTH(domain_name) - LOCATE('.', REVERSE(domain_name)) + 2) 


can be simplified from 4 function calls to 1:

SUBSTRING_INDEX(domain_name, '.', -1)