You don't say what the malware name was, but only true viruses (not trojans, etc.) can a repair be attempted, e.g. remove the small element inserted into the legit file. Trojan files are all malicious content so there is essentially nothing to repair. So sending it to the avast chest was the correct action to do.
There is no rush to delete anything from the chest, a protected area where it can do no harm. Anything that you send to the chest you should leave there for a few weeks. If after that time you have suffered no adverse effects from moving these to the chest, scan them again (inside the chest) and if they are still detected as viruses, delete them.
The differences between the free and paid version of MBAM is that the free version doesn't provide resident protection, it is on-demand scanning only.
There should be no conflict with avast with the free or pro version of MBAM. If you choose the pro version of MBAM, the only exclusion I would suggest you need it to enter the c:\windows\temp\_avast_ folder in the Ignore List tab of the MBAM settings. This is where avast unpacks files/content that it is going to scan, so you don't want MBAM monitoring that folder.
