Mac Mail App - Lot's of flagged emails: getting rid of it
Stars on Gmail are flags on Mail app. You can go ahead and remove the flags if you wish; the Flagged folder is a smart folder and removing the flags or stars will empty it. Or you can just leave them there, it depends on what you used Stars for. 

I wouldn't delete them though; while usually items in folders are just tags in Gmail, I'm not sure if deleting mail in folders will result in just removing the tag and keeping other copies on their folders, or deleting them for good; it will probably depend on your settings.