I think the problem is that we just don't know much about Peridot or Jasper's motivation or backstory. If we could learn about WHY they chose Earth over the billions of other planets to visit and conquer, maybe we could learn weather we should sympathize with them or loathe them completely. Time will tell.

Eh, I still go for the idea that she's just doing her duty. She is technically in the right in regards to punishing the Crystal Gems. You know, for starting a war, probably killed off a good number of Homeworld gems… What happened on the ship and in the ocean just kind of makes it personal now.

And we haven't seen much of gem society. How militarized it is and expectations to do what they're supposed to. It's not like she's a "wahahaha!" kind of villain. She even goes as far as to say she had a bit of respect for Rose's military ability.