I've configured PL to NOT exclude Malwarebyte's Anti-Malware's main scanning executable (mbam.exe) from Pro-Balance restraint, and while I do see in the log "Process priority temporarily lowered" during scans, unless I actually pause those scans, other foreground processes slow down significantly, especially in the start-up phase (ex: If I were to open Firefox during a scan, it takes forever for the browser window to appear).
Well, thats really just because its a scanning type of app, reading/checking HD so it is I/O intensive , does use some cpu but if you try and open another app then it has to stop or share reading from HD . That is a little different than cpu alternating threads/priorities .
You might try changing the ProBalance options (the configuration dialog for its params) to check 'Lower I/O priority during restraint' and/or 'Lower to Idle instead of Below Normal'. This might help some, though for I/O related bottlenecks, it is true that little can be done. Probably in your case the best thing you could do is move your page file to another drive, if one is available. That way the drive doesn't have to seek all over the place when a page fault (request for memory to be loaded from page file) occurs during a scan.