Oh yeah, SWORD having plans to take Wanda down is totally valid. From the outside looking in, she's probably pretty gods damn scary; started out as a terrorist and seemingly only switched sides when her own country was in danger. Accidentally killed people in Lagos, then became a wanted felon and spent years in hiding, then ripped a lab apart and stole Vision's corpse, which she then seemingly animated while taking control of an entire town. And she's taken down the Avengers by herself and would've done Thanos in if she had gone for the head instead of trying to rip him apart slowly. Yeah, Wanda is a scary mofo if you don't know her.
How the SWORD director (gods what *is* his name??) has gone about things is totally wrong and foolish, but I don't blame him at all for treating Wanda like a potential threat and taking steps to deal with her.
He might just be in over his head and incompetent but otherwise innocent, or he might be doing all this on purpose. I figure at the very least he was trying to weaponize Vision and is trying to keep that a secret (such a thing would fit the "sentient weapon" mandate and it's the kind of crap Fury would pull), but at worst he might be Nightmare or Mephisto or whoever's behind it all, putting up enough stress to make Wanda want to stay in West View. Hell, he might be a skrull. We know there's that upcoming Secret Invasion show, Woo mentioned them on his white board, and like someone else said, Monica trusted the guy before the Snap but so far he doesn't seem like he deserves that, so either the five years between blips were really hard on him and he lost his edge (possible) or maybe he got replaced at some point.