Whenever you take over a team as a mid-season replacement, ADMIN advises you that you are also taking over that team's record and that it will be reflected in your owner profile. To me, that implies that if you are not willing to take on the record, then you shouldn't be taking on the team.
I would guess that it would not be a trivial programming change to allow for team records to be split among multiple owners for a particular season.
You do have a couple of options:
(1) if you have an awful season on your profile due to a mid-season takeover of an abandonment, explain it to the commish when you are trying to join a private world. Unless they are jerks they should understand, because this is hardly an uncommon occurrence. If they are jerks, then consider that a sign that maybe you shouldn't want to join that world.
(2) If it really bothers you, create a second ID and run the mid-season replacements under that ID. If you plan to retain the team for future seasons, have the team transferred to your primary ID at or after rollover. That way, you have a "clean" ID for "your" teams, and a "dirty" ID for the mid-season takeovers.