Yes, you can do it two ways:
1) make a copy of the generator config file you're using and in there, change the first Description tag words, so you can recognize it in the generator configuration screen. Then, remove the task which generates the app.config file. Then use this generator config when generating code.
OR
2) make a copy of the template set config file you're using, change the name tag's contents so you can recognize it in the generator configuration screen and remove the template binding for the appconfig template. Then use this template set when generating code.
1) is recommended. 2) will work as well, but will give an error in the generator log, though generation will work fine (i.e. won't be stopped by the error).