Qawwali is a 700-year old tradition. Harmonium is a European instrument and was introduced to India quite recently, may be a 150-200 years back. But it plays a very important role in the Qawwali tradition.
Wikipedia explains the inconsistency. Sarangi was the instrument used in Qawwali prior to Harmonium. The new entrant was even better as Sarangi needed to come in between while this one didnt have to, and has quickly become the de facto accompaniment.
By the way, very few Indians know that harmonium is an alieninstrument. Interestingly, India has been the last refuge for this extinguishing instrument. To quote somebody, India is the museum of the British Raj. Brilliantly said, ha!