The original Japanese only had it as X must "fight" Zero, not so much kill, if I recall. Except it's not really very shocking since that was a thing in X2, so it all really ends up being very stupid.
As for Maverick Hunter...
Uh, guys? Inafune was OK with it to start with, you have to remember he was enamored with Western devs at the time. And the reason why he would be A-OK with it:
Maverick Hunter is the codename of a cancelled first-person shooter based on the Mega Man X series. It would have been a reboot of the series. Maverick Hunter was cancelled in 2010 but was kept secret until April 9th 2013. It was going to be a darker Mega Man X game themed around a new X...
megaman.fandom.com
I hope you are all seeing a pattern by now.