By the "allegro pop-up" do you mean the "license picker"? If you do, set a license default for the duration of running the scripts and ensure that one license token of that product is available, or use the "-product <product license name>" command line option to "just use that product license" for running the scripts. There is an enhancement request submitted to add a "use any license" mode command line option to run scripts without being prompted for a license, which will be OK as long as "some" license token is available to run allegro.
If you mean the "allegro UI" popping up, there is a "-nograph" option to run allegro without the canvas appearing but my scripts seem to have been ineffective when I have tried to use this option in the past. See the allegro.txt file in the product installation at share\pcb\batchhelp for allegro command line options, the "-product" option, and other options, are documented in that file as well.