To start, you're gonna need some background to understand who Chrysalis *is*.

Queen Chrysalis, originally Princess Terra, is the third and youngest sister of the Celestial Trinity. She represents, and has celestial domain over, the planet Eqqus (Earth).

After Her father's Banishment (a story of it's own, for another time), she attempted to take the reins of Gaia's Protector.
Gaia was distraught by His departure, and lashed out in anger, corrupting Terra and her contingent of Guards. Thus, they became the first Changelings.

Why would I forgive her deeds? Because they are not out of malice. After Her corruption, she sought out her sister Celestia. The look of horror and disgust upon the elder Princess' face was enough to drive Terra from the castle.

Similar situations arose upon contact with any of the civilian ponies. They looked at her and her guard like they were abominations. So they kept fleeing, far from any civilization. Into the arid wasteland known as the Badlands.

None know what happened to Her past that. Only that years later, whispers of strange shapeshifting beings matching the once-thought fevered description of Her transformed guard arose.

She acts out of necessity. Changelings, as you know, are Emotivores. And wastelands tend to not have sapient beings capable of emotion. They resort to subterfuge because it's the only way they can be around normal ponies to get what they need to survive. Stealing the form of a loved one is an unfortunate, but necessary, consequence. Contact with the Two Sisters has been attempted, to mend the rift between them, but upon the (necessary) reveal of Her agent's true forms, they are immediately detained before even laying eyes upon them.

Perhaps one day, they can come together as one. Perhaps not. Millenia have already passed, but only further time can tell.

(stopped watching in season... 5? Heard of some 'Ling named Thorax doing things, but that's the extent of my knowledge.)