I had an answer, argued with myself, lost the argument, consulted my inner child, and still had trouble deciding what to tell you.
Scaling from 1080 to 720 is not usually that bad. You might find that you like certain parts of the 1080 footage frames better than others and you might want to adjust to center the best part of the larger frame into the smaller frame size.
As long as you make that decision in After Effects before exporting it to be used in Premiere Pro, I believe that you will be happier converting everything to match in After Effects. I don’t believe that the generational loss will be as big a problem as trying to deal with different footage might be.
Only you can check it and find out for yourself. Play with a couple of different clips. One with lots of motion. One with very little. If it looks good, do it that way.