Membership High MySQL Usage

Have about 3k members registered on website with membership with different membership status like active, expired.

Membership 2 Pro has a Cron function for check membership status at every 6hours. Now issue is that it checks each and every user's membership status, and update membership accordingly so this cause a huge Mysql query, and brings the server down, every 6 hours.

Don't see any specific log, or server error related to this. But could notice high server load every six hours.

Would like to know any workaround to to fix how the cron checks, or anything helpful.