You can encrypt the SD card that has a home folder on it with FileVault. Open Finder, then right-click on the SD card and select Encrypt. On the pop-up window, enter your password information and click "Encrypt Disk."
After the SD card is encrypted, you'll need to enter the password to unlock it before you can access the home folder the next time you log into your Mac. To avoid the trouble, you can use BootUnlock to automatically unlock the SD card upon logging in.