doing anything to his lineup goes into the realm of "managing another person's team for them", and is a bad precedent. he's got all day to realize that he needs to pick up Prater. if he doesn't, then he deserves to lose. don't change anything, and don't even tell him. let him manage (or mismanage) his own team.
Most leagues have a rule that all teams must field a starting line up. Most leagues when you pick up a player and drop a player will insert that player in your starting lineup, especially when it's the only player at that position. Especially since it's a yahoo/family league I would say that this is not going down the 'slipper slope'/parade of horribles that you are describing.
He is not gaining any unfair advantage here, and in fact you are gaining an unfair advantage if you get to play 10 on 9 or whatever. This is as much in fairness to the other teams in the league as it is in fairness to him, actually probably moreso.
You don't set a precedent like this because it is easy for people to abuse, and there are people who will do so. All it takes then is one guy who drops his sole kicker for a Sunday early game kicker and leaves him out of his lineup. He watches to see what the result is and if he likes it he calls on the commish to fix his lineup. If he doesn't he picks up a later game kicker and puts him in his lineup.
How are you going to handle that? Are you going to force anyone who has an invalid lineup spot to take the best/worst player on their bench? What if the owner was waiting to hear late game injury info to make his pick up so it was legitimate that he was waiting? What do you do when someone drops his 7th string WR for a backup TE when his TE starter is doubtful, but forgets to start him? Are you going to remove the starting TE and insert the backup for him too if the starter doesn't play? What if the starter actually played, but you think his intent was to play the guy he picked up since he never carries backup TEs? Why would a league want to put themselves into the position of having to judge intent in situations like this?
If you are going to start changing people's lineups you need extremely clearly defined rules to do so, which obviously this league doesn't have. And even then they can probably still be abused. Better is to put the responsibility for the line up on the owner where it belongs. If you have an issue with an owner not setting a lineup, doing it for him is not the solution. Either replacing him as an owner, or coming up with rules that encourage lineups be complete (such as fines or future draft pick penalties).
The only time a commish should be setting someone else's lineup is when he is completely unavailable such as due to illness, family emergency, etc.
In this particular case especially it shouldn't be an argument. There is a kicker available, he can go correct his mistake himself. No commish action is necessary.