Added incentive?
Possible.

From a legal standpoint, John supplied the murder weapon, which, as has been pointed out, is likely unregistered and illegal. Another charge against John. The gun would be traced back to him, being military issue and whatnot. The only way I can believe that John didn't get wrapped up in this is that Mycroft made a fast deal with the Crown: you don't ask where my brother got the gun and you can punish him.

Again, I work in law enforcement in Canada, which has a legal system was based on Britain's, so I'm not pulling this out of thin air. I recently worked on two cases that were very similar to this. A junkie stormed a crackhouse and killed his dealer with a knife. The buddy who supplied the knife and swore up and down that he just gave it to his friend without knowing that the friend was going to do with it was indicted as an accomplice to the murder. In another, a guy drove the getaway car for a home robbery in which the robber inadvertently killed the homeowner during a struggle. The guy driving the car was also charged with second degree murder, although his charge was plead down to involuntary manslaughter.

Mary

That's also the reason why I think Sherlock won't have a problem if he returns ... for the public.
IMO Magnussen was officially killed be an unknown murderer.

The public aren't going to know about this at all.
Mycroft took his minions to apprehend CAM for holding private government property.
Those minions then witnessed a murder which their boss dealt with.
 

What an interesting topic! Here are my „two cents“ to it:
 
Sherlock wanted to get rid of CAM, but certainly not by killing him – he just wished to uncover his illegal blackmail material that contained some classified government information and have CAM arrested. During CAM´s visit to Baker Street he was mislead into thinking that CAM has this information physically, on paper, because CAM himself suggested it. Sherlock therefore staged whole „selling of Mycroft´s notebook deal“, but I don´t think he awaited that CAM will buy his story, nor did he care for that – his real objective was just to get inside Appledore. Sherlock probably believed that he will be able to uncover the place where CAM hid his vaults by his power of keen observation and then he will force CAM to give those blackmail materials up (or alternatively, he will just force CAM to wait until Mycroft´s men come and arrest him for possessing that classified information as a foreign spy).
 
And here is where a gun comes into the play – CAM was clearly panicked and willing to do anything when Mary pointed a gun at him, so why not use this easy method of threatening him? So, Sherlock orders John to bring his gun. Earlier, when they comitted burglary into CAM´s office, the gun was not needed – if John and Sherlock were caught there, the gun would incriminate them in a serious way. That´s not the case with Appledore where Sherlock planned to force Magnussen to give his vaults up, or, if that would not be possible, to act as a „concerned citizen stopping a foreign spy from escaping“.
 
The revelation that CAM has his vaults only in his head was therefore a catastrophe for Sherlock. He realised that he has lead John into a trap and that they will be both arrested for treason and leave both Mary and Mycroft at CAM´s mercy. But I still don´t think Sherlock thought about killing CAM immediately. I believe that he was just broken and badly shaken up. The idea of killing CAM only occured to him after CAM flicked John´s face. That was the last straw that did it and it pushed Sherlock towards self-sacrifice.
 
As to why John wasn´t accused as Sherlock´s accomplice – can it be that Sherlock confessed to gun being his own? He killed CAM in a way that left no doubt that John didn´t plan this, maybe he went further and actually incriminated himself by confessing that it was him who hid that gun in John´s coat? Just my theory, of course.
 

nakahara wrote:

The revelation that CAM has his vaults only in his head was therefore a catastrophe for Sherlock. He realised that he has lead John into a trap and that they will be both arrested for treason and leave both Mary and Mycroft at CAM´s mercy. But I still don´t think Sherlock thought about killing CAM immediately. I believe that he was just broken and badly shaken up. The idea of killing CAM only occured to him after CAM flicked John´s face. That was the last straw that did it and it pushed Sherlock towards self-sacrifice.
 

I still believe Sherllocks decision to kill Magnussen came straight away  when he realised that there were no vaults. Which other chance did he have to solve the problem?
What Sherlock did ... he deliberately waited for Mycroft and his men before shooting. To be sure that John wasn't suspected.
 

gently69 wrote:

Sherlock certainly did. You can see it in his face when he finally realised that there are no vaults.

For me this is the moment he decides to kill Magnussen. This and no other. The second he realises it is all in his head. CAM threatening John is just to make it clear to all of us. Sherlock knows it at once. 
 

Because it's John's gun,.ex-service I reckon.

And why should he keep it after using it for a murder? If it can be followed?

Yes, remember that from the pilot too.