AFNI warns if input datasets are oblique, but this warning can be turned off with the AFNI environment variable, AFNI_NO_OBLIQUE_WARNING, set to YES. You can align oblique EPI data to an anatomical dataset that is in a standard space with "align_epi_anat.py -tlrc_apar ..." That will avoid interpolating the data twice. If you want to remove the oblique information from any dataset, you can use 3drefit -deoblique, and no warnings will be shown when using that dataset.