Are you really sure you want an SUV with having 5 kids...???
The Atlas can only place two car seats in the 3rd row, and you'll be forced to place remaining three in the 2nd row.
In the Pacifica, if you can squeeze three car seats in the third row, then you can use the remaining two seats in the center and driver side 2nd row seats, leaving the passenger side second row stowed in permanently for easier ingress and egress.
In addition, you already know that with small kids come a lot more baggage while traveling. With all your interior space used up with car seats and kids (I know how quickly it fills up...
), you'll need more space in your cargo which the Pacifica has way better than Atlas....and you can use the stow n' go space for storage as well (You won't be stowing those seats with car seats installed). Any car's interior will feel really congested after fitting several car seats. You'll feel a lot better if you have a walkway in the middle or side with the minivan.
Kids and car doors do not mate well. Sliding doors are your friend here.
There is simply no way you can convince yourself practically that an SUV is much better than a minivan in this scenario. However, if you really like an Atlas and driving it makes you feel better, sure go ahead, accept the compromises and there's nothing stopping you. After all life is full of compromises anyway.
I'm sure you'd probably have seen this review which the Atlas wins.