What would killing Napoleon have accomplished, at least, killing him in such a public manner? You have to remember that, despite the risk that leaving him alive did in terms of leaving someone for a base of power to coalesce around, turning him into a martyr was even more of a risk, particularly when one wants to ensure a stable France for a reinstated Bourbon monarch. Better to exile the man and take the wind out of the sails of any possible revolt.

It's also important to note that, by this time, Napoleon had been Emperor of France for more than a decade. Murdering a monarch was not particularly high on the list of things other monarchs were interested in. Napoleon himself never ordered the execution of any sitting monarch, and the distaste in Europe caused by the murder of Louis XVII should be evidence enough that regicide was not exactly something undertaken lightly.

That said, his later imprisonment was clearly undertaken to eliminate him in a way that would not raise the hackles of the French people. Death by boredom, one might call it.