Doesn't really matter whether they intentionally left out the IFF, it takes an active action to launch the missiles so it was an intentional and malicious act fully intended to take down the aircraft it was aiming at.
They probably thought that it was a Ukrainian troop transport(which is a legitimate military target) but that doesn't resolve them of any responsibility or guilt whatsoever in whether they intended to shoot down a civilian airliner or not.
International law is crystal clear on that part, it lies upon every soldier to establish beyond any doubt that the target is not civilian(typically this is filtered down the chain of command through standing orders because ICAO goes out of it's way to inform nations what civilian air traffic will be crossing their skies), hence there can be no excuse or justification to shoot down a civilian target other than an electrical malfunction where the missile launched without being commanded to do so.
The rebels are thugs and terrorists and so are Russia for arming them(not to mention that Russia annexed Ukrainian territory, also in violation of international law)