Microsoft have special Scale Groups for “heavy” CRM Online instances. A higher scale group allows longer timeout period (60s increased to 120s, or 300s) and processing more records (50k increased to 100k).
If your CRM Online instance is experiencing issues related to these limitations (e.g. executing reports with more than 100,000 records, or using aggregate functions involving more than 50,000 records, etc.) and these issues are CEO-impacting, then submit a support request with Microsoft to request for your instance to be migrated across to one of the special Scale Groups.