How to make multiple GND pours in Altium?
Option 1: Just bite the bullet and make the AGND pour in an L shape.

Option 2: In the polygon manager, adjust the pour order so the DGND pour happens before the AGND pour. 

I'm not clear what you mean about "draw another polygon for cutting a square out of the AGND". If DGND is poured first, and your design rules are set correctly, Altium will respect the different nets clearance rule and produce a clearance between the DGND polygon and the AGND being poured around it.

However I actually prefer the first option because it is less likely to cause trouble if you edit the design later, shelve some of the pours, need to add a new polygon that overlaps the first two, etc.