Yes, the goal should be disallowed. It also makes no difference as to whether the ball has hit the ground (ie. for a dropkick rather than a punt).
The restart of play is an indirect free kick for playing in a dangerous manner, awarded to the goalkeeper's team.
The relevant information from the 2015/16 FIFA Laws of the Game, pages 122 - 123:
A goalkeeper is considered to be in control of the ball:while the ball is between his hands or between his hand and any surface (e.g. ground, own body) while holding the ball in his outstretched open hand while in the act of bouncing it on the ground or tossing it into the air
When a goalkeeper has gained possession of the ball with his hands, he cannot be challenged by an opponent.
A player must be penalised for playing in a dangerous manner if he kicks or attempts to kick the ball when the goalkeeper is in the process of releasing it.
and on page 38:
An indirect free...