Malir Cantt is pretty safe, it’s an army cantonment, with the Pak Army protecting the Area. Doesn’t matter if the city’s on fire, you won’t know about it inside the Cantonment. You’ve got the commute times right too. But I suggest that you research Askari 4, PNS Karsaz and PAF Base Faisal too. All these place are at about a 15 minute drive from Agha Khan.
I’m not too sure if PNS Karsaz(navy residential area) and PAF Base Faisal(The airforce) rent out to civilians, but these two are pretty much like Malir Cantt in terms of security, just smaller.
Staying in Malir Cantt you’d be too isolated from the city, whereas these places are pretty close to where all the action happens(the good kind, shopping, food, the beach, etc)