Well, it greatly depends on what the malware is. File Infectors can infect legit system files, but quarantining it kills it in the systems eye, but quarrantine gives you the option of restoring what ever you put there, making it the best default option, so you are in the right way of thinking about this.
False positives are a second reason to not delete right away.
As a rule to be super safe I keep anything quarrantined a month, but I would say a week is more reasonable. They can do no harm there.
Is it safe to remove files once it's been quarantined? Or if the infected files are important, would that hurt the computer once permanently removed? I have a bunch of files in quarantine because I don't know quite what to do with them.