Callao isn't a great area in general and there certainly are robberies along the main roads sometimes but its not a war zone. You have reliable transportation arranged, so lock the doors and dont fiddle with your phone and you'll be outta there soon enough.
Miraflores is totally fine. I think I've even seen a few single woman walking around at night, one or twice
It does seem there has been an increase in crime this year but it also seems like the chatter has been overblown. Still, you don't need to be overly paranoid. Just use basic common sense. It would be a shame to go and then sit in the hotel because you're afraid to go out.