Well, you cannot be 100% sure of anything can you now, however, a long time ago AV companies used to modify the Windows kernel in order to give them an edge over the nasty stuff that users may have unintentionally installed. This worked but also made system very prone to BSOD and general instability. Currently AV makers employ other means to identify and get rid of threats.
Along with an AV you should be using other ways to protect your data , like backups, either just simple file backup or system snapshots (images), which, in case something goes wrong will allow you to diminish the downtime caused while trying to restore your system. You don't need to be scared of your PC, you need to be in control.
Directly to the point: I also do not turn off Avast! while using Windows Update and one should not have to turn off AV protection to update system critical stuff.