AGT has support for Hatari Natfeats (Native Features), which is an API used to control the emulator. AGT leverages it as a means to display debug output, so if you don't want to use the on-screen debugging this is a viable alternative, and as an added bonus it's still visible while showing full screen graphics.
To enable the Hatari output you need to first make a couple of small changes in the Makefile. First search for the BUILD_CFG variable and ensure it's set to debug:
BUILD_CFG = debug
And then search for USE_HATARI_NATFEATS and make sure it's set to yes. If it's not there, add it.
USE_HATARI_NATFEATS = yes
Do a clean build and then launch hatari with --natfeats true - you should then see your logging appear in the terminal used to launch Hatari, rather than on the emulated screen of the STE. If you're staring at a white screen and wondering why, your program is still probably waiting for you to hit space ;)
make clean
make
hatari --natfeats true ./disk1