You know most, if not all antivirus programs let you whitelist programs you don't want deleted, right?
If you're using something that immediately deletes it instead of quarantining the program you're using, then it's probably not a decent program to begin with.
Here's my problems
A) Most programs seems to assume I'm an idiot, and refuse to whitelist the program; they accept, but immediately they'll re-add the program to the quarantine list
B) I have a LOT of apps in folders spread over 3 HDDs, and I don't want to spend hours whitelisting every single one of them in the off-chance I might actually use them
Furthermore, I don't like having a super complex firewall setup. I already have a hardware firewall which works fine, and a few Firefox addons to prevent crazy scripts from launching without my permission. I don't need additional software to try and control my net behaviour. They also have large filesizes for download (and my cap is not good), swallow RAM like there's no tomorrow and take time to disable or uninstall (usually making it unclear).
I have my system. It works great. The only issues I have to deal with are the occasional HDD failures (since they're getting old) and some scripts for different programs not liking other scripts. In my experience, anti-virus programs bring FAR more problems than they fix.