Fitz reacted to this by losing a hell of a lot of trust in her, in spite of his using her as his "affection object" in his hallucinations. So when he learns about Skye's powers, he has his freakout, gets over it -- and then begins assuming the worst about what Simmons's freakouts over Raina mean for Skye. Which, of course, hurts Simmons more than she can admit -- that Fitz has so much less trust in her than he used to. It's not fair of Fitz to react that way, anymore than it was fair of her to run away from him.
Um, lets see Simmons was trying to make a supersized version of the drug they use to knock people out dispute Fitz pointing out that it could have potential harmful effects,
A not completely unfair project to pursue, given that the effects of the icer drugs in their standard dosage may not be sufficient for someone with Inhuman biology.
recomended that if they should be will to just kill Raina,
That is not a coherent sentence fragment. But, assuming you meant to say that she recommended that Coulson's team should just kill Raina... no. That is not what she said. Her exact words were:
SIMMONS: I'm aware the team hunting Raina has orders to capture, not kill.
COULSON: As always.
SIMMONS: But this might be some sort of contagion or even a plague inadvertently set loose. Plagues must be understood, yes but eventually eradicated.
COULSON: Are you saying that you want to put Raina down, Agent Simmons?
SIMMONS: No, of course not, uh I'm just saying that if they have to, it may not be the worst thing.
It's important, again, to understand her mindset. She doesn't yet understand that the Inhumans are a minority, that their biology is natural for them. She sees it as a disease, as something that is potentially communicable and harmful. To Fitz (and to us), the Inhumans are "born this way;" to Simmons, they're like Ebola victims who present a health threat to people who don't yet know how to protect themselves from the virus.
She is not actively advocating for Raina's murder. She
is suggesting that it may be necessary to prevent what she believes may be an epidemic of potentially lethal mutations. Remember, she doesn't know at this point that the Inhumans were created by the Kree, nor does she know that only some Humans react this way to Terrigenesis mists. All she knows is that it killed her friend and mutated another into a dangerous creature that killed two of the men under her command.
She is wrong, yes. And her miscomprehension of the situation may yet lead to her developing anti-superpowered/anti-Inhuman bigotry. But she is not actively malicious or aggressive, either.
Edit to add:Remember, she uses the phrase "if they have to." Meaning, if they are unable to capture her -- and thus unable to quarantine her.
End edit.
though using drugs to dampen Skye's emotions were a good idea,
These last couple of episodes have revealed that Skye has not be successfully controlling her powers -- they've just been redirected inwards, creating hairline fractures in her body. Hell, Skye herself dampened her emotions during a "quake-fit" by injecting herself with an icer to stop the earthquakes.
Her suggestion is not entirely unreasonable.
So how exactly does Fitz being not exaxctly trusting Simmons a bad thing exactly?
He's not hearing her out, not really listening to her. He's projecting his own feelings of rejection (from the fact that she did not reciprocate his unrequited love and ran away from him) onto her, assuming that she's just going to reject Skye and be hostile. And in doing so, Fitz and Skye inadvertently endangered the entire team, since the team had no way of knowing they needed to protect Skye from the Kree agent or from Lady Sif almost until it was too late, and no way of knowing that Skye could cause dangerous earthquakes if placed in an emotionally stressful situation.
Which is not to say that the team has been handling Skye well, either. They've essentially put her into a very, very nice prison in the form of a cabin in the woods, when she is completely innocent of any crime.
It's not a situation where either side is clearly in the right or wrong. Simmons is wrong to feel so frightened of and hostile towards superpowers, but she's not as hostile as Fitz imagined -- she didn't reject Skye as a friend and ally the way he feared. And Fitz was wrong not to share important information, wrong to assume that Simmons was coming from a place of rejection and hatred, when in fact Simmons is frightened
for Skye as much as anything else, and seems to have abandoned her initial fears of the Inhuman mutations being communicable.