My thoughts:
1) Personally, I'm not huge on Waller turning your team into the Suicide Squad. Correct me if I'm wrong, but I thought the Suicide Squad was comprised of villains who'd been captured by ARGUS and forced into it. If that's correct, I think the more thematic way of doing it would be to allow Waller to turn your opponent's heroes into Suicide Squad members when you would destroy them (as in, you take control of them instead of placing the killing wounds).
2) I'm also in agreement that the destruction should be optional. However, I'd allow her to use it on all your figures, I could totally see her having fail-safes in place to take out her allies if they became a danger. In an old write-up of mine I had it as its own power:
NECESSARY FAIL-SAFES
When an opponent would take temporary or permanent control of a figure you control, you may reveal and remove an "X" Order Marker from this card to destroy that figure.
3) I'd like her to be a leader for Agents in addition to her Suicide Squad/Task Force X powers; if an ARGUS squad gets made, they'll most likely be Agents and Waller should totally be able to command them around.
4) I'm not completely sold on Behind the Curtain. I like the theme you're going for with it, but I don't think it translates well; as it's currently written, it feels like some sort of cloaking or illusion power. Plus I'm not sure its needed. You'll already be leaving her in the back of your base, which gets that feel of managing from a distance while also protecting her against most opponents.
My
.