...But now I'm leaning toward excluding them.
I agree on this, mainly because there was obviously a reason for them to be banned so I'd trust them (and their trust lists) less.
However I don't see why inactive users should be excluded. Their previous opinions/trusts/lists aren't less valid just because they're inactive. Maybe I'd trust their opinions/trusts/lists less if they
were active but didn't get any merit during those 3 years.
If the change is to be done and the choose is between 2 or 3 distinct users then I'd vote for 2.