If the players are to be whacked, the union has to buckle and that wasn't going to happen, hence the league took the most expedient route to get the answers, via offers of immunity in exchange for cooperation. MLB then quickly levied a punishment. We've also since learned the Astros were negligent in not informing the players about MLBs memo on warnings related to sign stealing. The players weren't going to get whacked. If the other players are pissed they can take it up with their union and the next CBA.
In the big picture I think it was well played by the league. They got to conduct and finish an investigation and levy penalties very quickly. Not perfect, no, but this outcome from MLB perspective was pretty good. This won't be hanging around MLB all summer while they fumble through an investigation wo player cooperation. The deflate gate debacle which carried on forever among other keystone cop routines were great lessons.
