> Is this something a reasonably fit person should be able to accomplish in an hour’s time? 

Hard to say and it depends a lot on your details. Do you have checked luggage, what class are you flying, do you have status, what passport do you have, will your flight be delayed, etc.

This being said, the trains from Copenhagen airport to Malmo go fairly frequently (20 minutes if I remember correctly, unless  there is construction, urggh) so if you miss one, just take the next. You can buy tickets at the airport at the ticket machines, but they can have long lines. So pre-buying a ticket is a good idea. 

> Also, is a short walk (3 blocks or so) in Malmö late evening safe?

Yes. Sweden is very safe and this is not all that late. Also, most Scandinavians speak excellent English and are quite friendly, so you will not have any problems communicating.