Your question is in essence "should I delete an operating system I no longer use". Sounds like a no-brainer to me. To delete it the absolute best way is to BACKUP all of your files except the operating system on another hard drive, then format the laptop one completely. Then put the files back on it. If you just delete the windows folder you're still going to have a ghost operating system on it (you won't delete the boot sector for example, which can cause huge problems and possibly unexpected data loss).