I think you need to draw a distinction between 2 situations involving inactive owners:
1) The team's active roster has players who are injured, demoted, or have lost their job in the starting lineup. In this situation, I think it's totally fine for a commissioner to step in a make the roster "legit" as best as possible using the team's bench, as long as it's clear to everyone up front how long a team has before the commish can intervene. I would draw the line at adding replacement players, though.
2) The team's roster is filled with players who are way underperforming their draft position, but is still "legit". Not your problem. It sucks, but I would not touch the roster. It's not your place to make decisions about quality.