Yes a limitation of the free program requiring interactive input, the programmers have to eat
Your only option is that outlined in my last post. This only lasts for that scan and isn't carried forward to subsequent scans.
Once you get over your first thorough scan the likelihood of viruses detected on subsequent scans is reduced as the resident scanners should hopefully catch it before it arrives on your HDD.
Archive (zip, 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. Thorough is also by its design very thorough and perhaps a little overkill for routine use, were a Standard scan without archives should be adequate.
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.