This is a tough situation because you've got owners from last year who may have designed strategies based on the "2 keeper" rule for the upcoming season. I think if you decide to take away those 2 keepers by whatever measure, somebody is going to be pissed.
Instead of affecting the existing owners in the league, I would look for something that can benefit the newcomers without directly harming an existing owner. How about each existing owner declares his 2 keepers and all the other players get put back in the pool. Then have the two new guys do a serpentine mini-draft where they each make 3 picks (to compensate for the lower quality of keepers they are receiving) and then start off the regular draft in whatever the regular order will be.
Old owners will all get to keep their 2 best players so no one will feel robbed. New guys get an extra pick so they don't whine about getting leftovers. The new guys would lose their picks from the last round.