They also used urine for extracting Woad, and apparently, that smelled pretty bad too, I think it was Elizabeth 1 had some kind of a law enacted that kept Woad production several miles from anywhere she might be living because of the production smells.
You need not worry much about "residual" Ammonia in clothing after the wash, as Ammonia is one of the most water-soluble gases around the rinsing process should remove it all. Another benifit of putting it in the was is it will degrease the pipework in your washing machine and help keep that clean too!