This issue was pretty neat. I am so ready for a lot of these plots to implode in some messy ass way.
Regarding the Emma of it all, I'll just put my two cents here:
Charles and Erick going to Emma makes sense at the beginning of HoX and here, they are playing with politics and manipulation and that's just Emma's resume. Any other more trustworthy person would likely not go along with what they're doing. I mean this issue seemed to basically imply that the missions against Orchis are being self sabotaged in some form. There's more going on here.
As for Emma's reactions, I ask you to consider two things: One, being trauma dump thousands of years worth of memories where your species ends up in a terrible way + realizing that the events of your life have been manipulated for years is probably a lot of take in. Emma is only a mutant after all. She is allowed to have a bad reaction to that. Hence changing into diamond, a thing she does when she knows she's being emotional. And two, she didn't say she wouldn't go along with it, but given the reveal she is just not going to be loyal to them, which seems to me a reasonable response when you find out your colegues are probably even bigger manipulators than yourself.
As for her calling them out, is not unreasonable. She calls herself out all the time. She had Kitty join her team so Kitty could keep an eye on her. Emma is well aware that anyone moving the chess pieces can slip onto the bad side if they let themselves do it, and she just found out the leaders of mutant paradise are doing this on a larger scale than she probably ever imagined.
I think this will definitely lead to a shake up in how the mutant goverment if going to operate from now on and I'm eager to see how that plays out. I think the Council is going to work very differently than how it is here soon.