I like your idea of replacing these teams to make the matches meaningful. But a 3 or 4 star teams with players in correct position is likely stronger and more stable. This may not be fair to the teams which need to face them.
It's an example, the roster of a bot team, you know.
Full of 3* players and a couple of 4-5*.
An active, 35T manager can have (at least the started 11)a team of 4* players and with good coaching can win those teams.

Just one word relegation.
An abandoned team will cause the same problems to every level.

My proposal is replacing by a bot team and freezing till the manager would be active again.