i just did what the OP's commish did, as i think it's the most equitable way, especially in lieu of a bunch of non-returning teams.
my league is a 13-team standard 5x5 with normal drafts/waivers and, of course, 6 keepers. last year i recruited a bunch of people who hadn't played roto, if not fantasy baseball, before so basically they petered out by june/july and decided to not come back. that left me with a situation where if new players inherited teams there'd realistically be 2, if not 3, teams that everyone would want, and the other ones would leave the new guys starting at a disadvantage. considering that i ended up having to incorporate 6 new teams into the league, i decided to go the supplemental draft route.
i manually (and painstakingly, i might add) listed all of the players from those non-returning teams and made a wordpad document that i uploaded to paste-bin, instructing the kids to go and rank those players from 1-25 so i could use it akin to a yahoo pre-draft rankings list and manually do an auto-draft for them. i made sure to indoctrinate all of the new-signees to that list, altho the 2 who had signed up b4 i made the list seemed to be too stubborn to accept my IMs (/msg's aka /query's on irc) so in the end i got to experience the joy of arbitrarily ranking 25 players like that, although for fairness' sake i scrapped that and just went by yahoo o-rank, which is exactly what would have happened if they didn't make pre-draft rankings and allowed their draft to go the autopick route.
it worked out fairly well, insomuchas everyone has 6 pretty solid keepers (altho idk why some people would do odd things like ranking torii hunter #3 on a list with braun, cano, strasburg, d-wright, prince, etc) and they're nice and balanced out. one of our players last year decided to "troll" the league by going ahead and cutting all of his would-be keepers in september, allowing still-participating teams to use the WW to nab guys like carlos gonzalez, clayton kershaw, and/or yoenis cespedes. his team was left as a joke team chock full of players like vladimir guerrero, who didn't play in the majors last year..... and, of course, this guy was one of the first to sign up for this year and be all rah rah rah ready to go, which put me in a position because at least 2 other people flat out refused to play if i allowed him to stay in the league (TALES OF AN ABSENTEE COMMISSIONER, PREMIERING SUNDAY NIGHT ON LIFETIME: TELEVISION FOR WOMEN!)
AHEM. so yeah long story short, even tho i'm currently vexed/flummoxed as to how i actually get the list of which team wants to keep which players (as the manual draft took merely has a list of all the players yahoo o-ranked from 1-999 with black K/keeper icons next to their name but NO CLUE AS TO WHICH TEAM THEY BELONG TO) once i figure that out i'm sure that the supplemental keeper draft will be a slick way to go. again, it's one thing if you're trying to fill 1-2 spots in a 12/+ team league and the non-returning teams are fully worth inheriting and not liable to start off the newcomers at a disadvantage, but when you've got a big mess like i had i truly believe the most equitable way to go is to work out a way of liquidating all of the non-returning teams and having the new players go at it as democratically/fairly as possible. if you're able to sync up all of the new teams via a chat or something, then that's fantastic and you can do it live, otherwise the manual autodraft is relatively painless to do, that is, if you've gone and ranked everyone by their yahoo o-rank or your own personal rankings which will then apply to anyone and everyone who didn't give you the list.
or hey, if you're actually the commissioner maybe you can convince the league that what's most fair is you being rewarded for your hard work and getting mike trout as a tribute? jeeeeeezuss i wish i thought of him last year =/