Penalize him when he returns.
I see where you are coming from, but unless you are actually willing to start penalizing people for missing/sitting out hands, I don't think you can make this (huge) change.
Practically, I think if you start penalizing people anytime they've missed a few hands, on top of the 'penalty' of already surrendering their antes, you are really going to get people mad (even more mad than with the first off the deck rule!)... not to mention the fact that TDs would be kept super busy simply assessing penalties to people for missing hands. So I don't think it is practical to penalize players simply for being absent. They should be able to choose to be away from the table, so long as they satisfy their obligations (i.e. posting all forced bets).
It follows then that if I know that I will not be penalized for missing hands, and for example, it's getting really close to a money bubble in a Stud or mixed game tourney where I plan not to play any hands until the bubble breaks, I now have a huge incentive to leave the table and sit out if your new rule meant that I would never have to post a bring-in while I am away from the table. I don't think that's very fair - if you are being dealt cards, as you will be in every hand of a tournament whether you are at your seat or not, you should be obliged to pay the bring-in if you were dealt the lowest card, period.
Now, with respect to how it affects the deal on fourth street, etc., I think the current procedure is OK the way it is (i.e. take in the hole cards of the absent player, killing the hand, and keep dealing upcards to that seat until it faces a bet that it cannot call). However, if you were really concerned about the way that this is done and think that it is too confusing, I think the better solution would be to change the procedure so that once the absent player brings-in and action moves on to the next player on third street, we immediately kill the absent player's hand
including mucking his upcard. I think this addresses most of your concerns without giving the absent player a free ride (well, a potentially discounted ride), and I would support that change if you proposed it. The reason that is often given for not doing it that way is that is potentially affects the order of the cards that would come out on fourth streets (and possibly beyond) if the bet is not actually completed on third street -- but since all the cards off the deck are random anyways and there are no game security issues because the dealer is still burning a card, I don't see that as a persuasive argument. It may indeed be simpler just to kill the hand of an absent player outright after the bring-in -- easier for the dealer and arguably more consistent with the way hands of absent players are immediately killed now in Holdem.