Exactly, because she was trying to cover up her involvement in the Enchantress mess. That's why she shot all the people in the room. She had to get herself out of there.
This doesn't make what she said at the beginning to the government a lie. She didn't predict Enchantress would go rogue and turn into a major threat against them.
Which they were. She didn't count on Enchantress turning against them. She thought she had her under control because she had her heart.
Because she is the most powerful. Nowhere in the movie is it implied the rest of the Squad wasn't going to be used to aid in this assault.
Because Waller was more concerned about herself than humanity. She was only interested in absolving herself of any link to the Enchantress mess by getting herself out of there safely, and killing any potential witnesses who could shaft her.
Pull the other one. Waller could have entire trained armies under her control if it was just about having people to control, who would be 50 times easier to control and rely on than a hit man, a fire freak, the Joker's gf, a crocodile man etc.
You have no basis to believe she was lying. She didn't make up any BS about the rest of the Squad members when she was selling them to the government, so why would she with Harley? If she didn't really believe Harley was up to the job that she had to make up crap about her, she wouldn't use her in the first place.
You certainly have no basis to believe to she never intended them to deal with metahuman threats. She had them directly dealing with metahuman threats.
First sensible thing you've said
If she was lying about anything, it would be shown. Otherwise how do you establish a character is a liar if you don't show the audience.