Humanitarian intervention doesn't challenge sovereignty through its meddling with domestic politics, but through its misunderstanding of those politics. Hypothetically, the United Nations may have been able to temporarily suppress the genocide in a country like Rwanda. However, it would not even begin to address the ethnopolitical roots of the fractures in that society.
A clear example is the Syrian civil war. Despite President Bashir al-Assad using biological weapons against his people, the United States had their hands tied. Among the combatants in the civil war, there was no clear ally for the US to support.
The government was corrupt, some of the rebels had ties to terrorist organizations, and many other barriers made an intervention impossible. Most notably, the more than a decade of conflict in the middle-East made many would-be rescuers wary of intervention.
As virtuous as an intervention may be, it is often merely a bandaid. Unfortunately, the domestic politics of a foreign country are often too complex for an intervening power to understand.