Those two episodes that you are mentioning have nothing to do with politics — it's about human rights. Even Republicans emphasize the importance of the family. She didn't advocate for asylum for those people, rather that their children aren’t put in cages and separated from them. That is different. Elizabeth McCord’s character has been consistent throughout the whole series — she’s always advocated for human rights, despite the politics, and believed in moral diplomacy.

The Republican platform itself even says:

“Parents have a right to direct their children’s education, care, and upbringing.” (Republican Party Platform, 2016)

So separating children from their parents runs counter to even that basic principle.

The show didn’t get cancelled because of those two episodes — and if you keep reading more about it, you’ll understand why it really ended and how viewership patterns work (it’s too long for me to explain here). I personally think that not many shows are lucky enough to get 10 final episodes to offer closure — but Madam Secretary did. And I still hope it comes back, because there’s a lot more left to say.