Sorry if mentioned and correct me if I am wrong but....
The plane was airborne 6 minutes after it's scheduled departure, yet there were 5 people who checked in but didn't board.
I find it hard to believe that after waiting and waiting for 5 people, you would then be able to find all of their luggage and remove it without delaying the plane
I don't find this suspicious at all. KUL is MH's hub, and as such people most likely connected to this flight from all over South East Asia/Europe/Australia/India etc.
It is possible that the these passengers were proactively denied boarding by MH in advance due to missing minimum connection time (eg if a connecting flight from BOM was delayed - pax would be offloaded).
I haven't read anything to say that this isn't the case. Likewise with many MH flights departing from KUL around the same time, I doubt 5 pax failing to board is statistically significant. They may have been simply fallen asleep etc.
Regardless, due to security reasons of course bags must be offloaded if passengers are not travelling, and it sounds like they were.