Even if the diet is vegan, if the diet is not toxin-free there will be smelly poops :(
If youre giving only organic foods, then start eliminating other sources of toxins...and the 'smelly' will lessen.
Other toxin sources: all the "whites" (sugar, flours, table salt ), all additives & preservatives ; all chlorinated/fluoridated water, virtually all soy products are especially toxic, especially to little ones (no soy 'milk'!) - and of course household cleaning/personal hygeine products.
Non-organic beans are smelly. Even organic beans make a smell like you report. Sprouting the beans for a day or two (before cooking) will eliminate the bean possibility.