I don't know about killing the agents, but there have been known examples of that kind of false flag terrorist attack. Probably the most famous is the Lavon Affair, but there's also:

• Operation Himmler.
• The Panda Bar Incident.
• The Miami Showband murders, although that was carried out by rogue soldiers rather than centrally directed.

There have also been a number of false-flag incidents in which a government attacked its own people with terrorism, but, whether by luck or by intention, no-one died:

• Operation Labrador.
• The Mukden Incident.
• Celle Hole.

There are also various well-known incidents that look like false flag terrorist attacks by a government on its own people, but which are disputed:

• The Baghdad Bombings (very similar to the Lavon Affair, but still denied).
• The Reichstag Fire.
• There are persistent and credible allegations that the DRS carried out false-flag terrorist attacks during the Algerian Civil War.
• It is possible that the 1999 bombings in Russia were a false-flag attack, but this incident is so bitterly contested that it's impossible for me to know what to make of these allegations.

It is also possible that there were other such incidents but where the false-flag activity went undetected.

Overall, such false-flag attacks seem to be extremely rare, but not unknown. They seem to normally occur in the context of an existing violent conflict. As we have no particular evidence that the Charlie Hebdo attacks were a false-flag operation, our prior that the French government was involved should be extremely low.