The correct way to clean is to boot from something clean (a bootable CD or USB) and then disinfect. Boot from that Windows again only after you cleaned it.
Yes, you're right. He needs to do a clean boot, as you say, with either an anti-virus rescue disk or even the OS disk. The best option is the AV rescue disk if one is available, but most people do not make one. (I don't think I have a current one.)
Second best, IMO, is to boot with Hirem's Boot CD (or similar) and run the AV scan from there. That will take care of the bug. Then he should be able to boot normally. He can download and burn the Hirems Boot CD on another PC.
After the PC has been thoroughly cleaned, he can add a good copy of MWB back onto the PC.
Running Malwarebytes on the PC that you are running your wallet on ( in addition to some well-respected brand of updated, ant-virus software ) is definitely a VERY good idea. It's the source of the MWB program that was the problem.
Even the "Free" version of Malwarebytes offers you some additional protection. They have just released a new version and if you are licensed under the previous version number, your old license key is still valid until your original subscription date arrives.
The new version is $39.99 per year. If you get the two-year subscription, they will knock 25% or $20 off the two-year pricing.
That's pretty cheap to protect your data and who-knows how many $$$$ of BTC's.
Anyway, download the newest version and choose "Trial" when you install it. That way you will get the full, premium editions full protection for 14 days. At the end of the 14 days, you can either pay for it and keep the premium version protection features or stay with free and it will continue to function in free mode.
Can't hurt to have the Premium protection for free for 14 days. I run the paid Premium Edition on the PC that runs Bitcoin Core and my wallet, and the Free Edition on my other laptops/PC's.
Here is a link to the new versions download: https://www.malwarebytes.com/
Don't take chances with your data or your Bitcoins!!! But you know that, as I'm sure your intentions were good to be running MWB in the first place.
Good luck and best wishes!