Two recommendations:
1) Have a whitelist that allows for groups to not expire, or a powershell parameter on a group that excludes from expiration. If the community agrees, please vote for this on user voice here:
https://office365.uservoice.com/forums/286611-office-365-groups/suggestions/31010725-office-365-groups-expiration-need-exclusion-feat
2) Have the expiration email notification only send out if there is no group activity occurring. For example, no files accessed or uploaded, or no emails sent/received. Currently, groups can expire even if they are actively being used for email or sharepoint. The risk is if the group owner doesn't see three emails then the group could be deleted. If the community agrees, please vote for this on user voice here:
https://office365.uservoice.com/forums/286611-office-365-groups/suggestions/33646915-expire-groups-based-on-inactivity