Okay so Shepherd ISN'T subtle and honestly I don't believe she loves Roman or Jane, or ever did.
Start with their names. Renaming children you adopt is a red flag in itself, essentially stripping them of one of the only gifts their original parents were able to give them. But renaming children as old as Roman and Remi were, who lost their parents due to violence the way they did, is downright cruel. It's an excision of their life with their parents, and the start of her molding them into what she wanted. Shepherd adopted them for herself, not for them. She raised them from childhood to be soldiers, not loving or happy people. And the names she chose for her "family" are also very telling.
First, her own name. Shepherd. Someone who guides the herd. Then Roman and Remi...it's giving Romulus and Remus, the twins who founded Rome. They were the children of Mars, god of War. They were abandoned at birth and adopted by...a shepherd. At one point in their story, Remus is captured by the enemy and rescued by Romulus. But ultimately they fought over where to establish their great city, and Romulus murdered Remus and became the sole founder of what would eventually become the Roman Empire.
Not only was Shepherd setting up her "children" to be her generals in the war she wanted to start, I believe losing Remi was not just a possibility but part of her plan. Roman is volatile but malleable, a follower for both Remi and Shepherd. But the Remi we see in flashbacks was a natural leader in ways that would be threatening to someone as manipulative and controlling as Shepherd, who claims to want an end to corruption and tyranny...but does she?
In the flashback with a young Kurt, I'd argue she lets her true desires slip. What she truly seeks is power. She doesn't want to take boots off necks, she just wants to be the one wearing the boots. And she doesn't want to be the face of power, but she does want to be the one pulling the strings. If her plant succeeds, she'll be the face of a revolution and can "cede" power to her handpicked leaders...but she'll still have the firepower and leverage.
But Remi is a staunch idealist and true believer in the cause who still does care deeply about other people. She was always going to see Shepherd for what she is eventually. Hell, maybe she did, and we just don't have that piece of the puzzle yet in season 2.
The point is that Sandstorm could have gotten those clues to Weller and his team in other ways, arguably ways that would be less messy and full of unexpected problems and variables. Erasing Remi's memory mainly serves one key purpose: it eliminates a threat to Shepherd's power. Either Remi becomes someone vulnerable who can be more easily manipulated, or she dies in the course of the mission.
Either way, Shepherd wins.
