Seems to me that Rosenberg is writing him in more a "let's take everyone out before dying" way, that is kinda the solicit for UXM 14 and he tried to do that in this issue. The things from him I've read are more darker than most comics, I didn't read New mutants, but astonishing X-men even while on the surface it was lighter everyone was completely broken (and in the last issue he mentions Scott with Havok desiring his approval and mentioning how he didn't smile anymore towards the end) and his punisher is dark (and one of the punisher comics that I can not only tolerate but like)
The logical thing would be that he considers the beggining of the war with the inhumans the destruction of the murder cloud (and it kinda was, it mentions that Storm got a truce at that time) and I don't know if Jono was with the X-men after the event of IvX (I didn't read much of the comics at the time)