Lincoln could barely neutralize Deathlok. If he's suddenly flying around blasting quinjets out of the sky while he's still recovering from what Hydra put him through it will be pretty fucking stupid. I have no doubt that Daisy could fuck them all up herself if she was really motivated, but I think she has too much faith in Coulson. She'll likely believe that Gonzalez acted against Coulson's wishes and do her best to defend Afterlife from SHIELD as non-lethally as she can, until she finds out that Jia Ying lied/sees Cal going berserk on the Hyde Formula, then she might really cut loose. I could also see Cal being so far gone on the formula that he actually goes after Daisy, which would end their relationship once and for all and probably push him the rest of the way over the edge once he found out. I'm sure he'd still find a way to blame Coulson though.
Only way Daisy doesn't figure out what Jia Ying did yet is if the writers decide to have her stay with the Inhumans instead of rejoining SHIELD, in which case it will end up being some huge reveal where Daisy turns against Jia Ying during the mid-season finale of season 3.