You can remove raster from GeoPackage with ogrinfo but it is a bit tricky because each raster table has also references in several metadata tables.
Drop the tiles
ogrinfo -sql "drop table raster2" droptest.gpkg
Remove line from gpkg_contents
ogrinfo -sql "delete from gpkg_contents where table_name='raster2'" droptest.gpkg
Remove references from gpkg_metadata_reference table. Ogrinfo does not accept the command with the same syntax as above because the SQLite database is now in invalid state because of orphaned foreign key constraints and you must use a special GDAL configuration option to override the validity check.
ogrinfo -sql "delete from gpkg_metadata_reference where table_name='raster2'" droptest.gpkg --config OGR_GPKG_FOREIGN_KEY_CHECK OFF
Remove references from gpkg_tile_matrix table.
ogrinfo -sql "delete from gpkg_tile_matrix where table_name='raster2'" droptest.gpkg --config OGR_GPKG_FOREIGN_KEY_CHECK OFF
Remove references from gpkg_tile_matrix_set table
ogrinfo -sql "delete from gpkg_tile_matrix_set where table_name='raster2'" droptest.gpkg --config OGR_GPKG_FOREIGN_KEY_CHECK OFF
Now the raster table and all the references have been deleted. As a final step it might be good to vacuum the database.
ogrinfo -sql "VACUUM" droptest.gpkg
However, if the database is very big VACUUM will be slow. It could actually be faster to copy all the raster layers except the one that you want to drop into a new GeoPackage with gdal_translate. If you have also lots of vector layers in your GeoPackage that option may not be so fascinating. For simplifying the deletion you can save all the ogrinfo commands into a batch file and give the name of the raster file that you want to drop as a variable.