Some thoughts.
1. Undemocratic rulers are illegitimate in principle.
2. Despite 1), they are quasi-legitimate in the sense that they can be acknowledged as “legitimate” actors for the sake of diplomacy etc.
3. Deposing an illegitimate ruler is OK, unless
4. his deposition brings more easily foreseeable troubles than his staying in power.

Saddam was not a legitimate ruler. But the disastrous results of his deposition were too easy to predict.