Format Linux partition USB SD
This will erase the partition to make it visible in Disk Utility(change PartitionName to whatever you want and see below to get DiskIdentifier):

sudo diskutil eraseVolume JHFS+ PartitionName DiskIdentifier


To get DiskIdentifier, Run diskutil list and find the partition you want to remove. DiskIdentifier is in the IDENTIFIER column.

Now you should be able to remove the partition in Disk Utility like normal.