Yes a bootable PE is the answer I think. I used to monkey around with them for ages. It was a matter of honour, but too many people have screwed up on me, so I perform an Acronis restore, either from a PE or from the Acronis boot disc, having first formatted the drive, shut down and cold booted. Leaving nothing to chance.
Why I'm so hardline on them; on one occasion, a Windows 98 machine, someone executed an attachment, but had the wisdom to instruct the firewall to permanently disallow the malware, as taught. Booting from floppies I fixed it. Having fixed it I couldn't remember how I fix it during the post mortem. I infected it again and couldn't fix it. So I use a steam hammer to crack the problem. Restores only take a few minutes; users have 10 minutes to recover their files and then it's my turn.