
Personally I don't use silent mode, because I want to know what is going on with my system. If someone is getting so many warnings of virus infection, infected emails, etc. that they become intrusive, then it is time to review their security practice - filter emails at source, delete from server rather than download them, etc.
I use MailWasher Pro to scan and delete from the server before downloading the remaining email with my email client. There is a freeware version of mailwasher which can be used on a single email account.