It is hard to say as we really don't know why it happened as there insufficient information.
Personally I don't do thorough scans or enable archives to be scanned.
Thorough is also by its design very thorough (it scans all files) and perhaps a little overkill for routine use, were a Standard scan without archives should be adequate. Archive (zip, rar, etc.) files are by their nature are inert, you need to extract the files and then you have to run them to be a threat. Long before that happens avast's Standard Shield should have scanned them and before an executable is run that is scanned.
I have only ever done a Through Scan with Archives once shortly after installation just to ensure a clean start state, but with XP for example avast will do a boot-time scan after installation if you select it, this I believe will be quicker and reasonably effective. Like everything in life things are a compromise.
Not sure what it is you are talking about when you say how do you overcome it in the future, depends on what 'it' you are talking about; avoiding the problem of the freeze (not enough info, see below) or stopping avast and not bumping into the self-defence (by temporarily disabling it).
Have (or did) you another AV installed in this system, if so what was it and how did you get rid of it ?
What other security applications do you have installed, anti-spyware, firewall, etc. ?
What are your system specs; OS ;CPU ;RAM ;Hard disk size and how much data, etc. ?