You are asserting that she actively wishes to either kill superpowered persons, or to conduct cruel experiments on them. The evidence from the show does not support either assertion.
But Simmons did not yet know any of that. She only knew that an alien tech killed one person and transformed another; she had no way of knowing that this wasn't a dangerous, communicable disease, and that was as reasonable a hypothesis as any given her limited information.
Oh, yes, a super power giving Virus was definitely the rational explanation

She definitely talked about doing a lot of tests, and she would have kept Skye locked up forever if she could have. And she obviously wants to kill super powered people, because she wouldn't shut up about killing Raina, and she wasn't saying it because of something Raina had done to Coulson ages ago.
Like I said, the fact that she didn't instantly join Mockingbird, is a point for her, its the first good thing she's done since Skye transformed.
No, I'm not saying that. But, the dissent certainly makes her seem more on Fake SHIELD's side, and she was definitely unsubtle about how far her ideas about things differ from Coulson. If Coulson's group was the only SHIELD, it would probably be something she'd change her mind on if she was around Skye enough. But now I can easily see her betraying Coulson, since Gonzales's team is doing exactly what she wants.
I'm not saying that she is against Coulson, but I doubt she would have supported him if he started getting too friendly with a super powered person. I will point out that, for all they knew when they first confronted Mac/MB, Mockingbird/Mac could have been HYDRA, so it would make sense for Simmons to take her out, even if Simmons isn't super loyal to Coulson. Simmons is a lot of things, but even I'll admit she's not a HYDRA supporter.
She had been a longstanding friend. And not once did she say that she thought their choice to infiltrate and attack the Playground was justified or appropriate.
ETA: And I think you should note that she consulted Fitz before deciding to provide medical treatment to Mack. And Fitz told her she should. So she acted to provide medical care to an injured man--who had injured himself to protect a member of Coulson!SHIELD--only after consulting with a thoroughly loyal and pro-superpowers teammate. Or are you going to claim Fitz is evil, too, now? End edit.
Fitz, if anything, is too sympathetic towards evil people, showing Mac more compassion than Simmons has shown Skye, but I don't hold it against him. Simmons would have helped Mac anyway (although I wish Mac had just never recovered, at least his death might have redeemed him a little).
As for her friend, its like the HYDRA thing. The academy agent is no longer a friend to a real SHIELD agent, she's just like Mockingbird or Ward. A traitor to SHIELD, and one that needs to be put away, not cooperated with. Simmons should be looking for a way to disable her and escape, not look at a traitor's injuries. At the very least she should have told her off, or said something against her.
If Simmons hates Skye, why did she go to all the trouble of trying to develop an advanced technology to heal all of her fractures? Why did she tell Skye that she cares about her over the SHIELD!Skype?
Simmons developed gloves that suppress the powers she hates, and also causes negative effects to Skye (skye complained about beeing dizzy after putting them on), which would make Skye easier to put down if needed. As for her talking to Skye, that could be a bunch of things. A cover so that Skye will start trusting her, lip service for anyone who could be listening to their call, and yes, maybe even a sign that Simmons might grow out of being a bigoted idiot.
Like I said, taking out Mockingbird, and looking at Fitz before helping Mac, could be the start of Simmons redemption. If she completely recants her bigotry against meta humans I'll go back to liking her, but she hasn't reached that point yet, and I can see her going in many different, bad, directions.