1.) Be upfront about what you will do
2.) Be vigilent and not allow some weeks to slide before acting
3.) Declare what 'projections' you will use
4.) Warn owners (via email best case) if they are approaching such an inactive period before gametime. Standard message should be cut and pasted such as "you have 1 or more players either injured or on bye for this week. If this isn't corrected by kickoff I will have to reset your lineup to best projected as agreed upon before the season."
As long as you are doing all of this, I'd ask him how he'd feel if 3 teams got 2 freebies in their division and the other 8 only got 1 from this inactive team. I wouldn't want to be fighting for a wildcard against one of those teams with an extra free game.
Oh, and I'd consider adding:
5.) Boot such inactive owners after the end of the season if there's not some type of serious excuse for inactivity (illness, etc.)
34-17/ 29-7 / 34-13 / 27-17 / 31-17
2010 & 2011 Baseball National Champs
Cause if my eyes don't deceive me, there's something goin' wrong around here.