The whole controversy regarding Sai Baba was quite unnecessary to say the least. Dwarka Shankaracharya need not have expressed his opinion, even if he felt very strongly about it. Hindu or Muslim, Sai Baba is the object of affection, adoration and devotion for millions who consider themselves Hindu and do not seem to bother about the religious convictions of Sai Baba. Hindu Seers supporting the Shankaracharya's views have sought to highlight scriptures and various 'acts' of Sai Baba which seem to indicate that he was not a God. Needless to say, it has not helped further their cause. What is even worse probably is the fact that millions of adherent Hindus who believe wholeheartedly in the Sanatan Dharma, seem totally unconcerned with the whole controversy. Imagine, The utterances of a Holy Seer going unheeded this way!
But then that is how the Hindu religion is! Diffused, Omnipresent and yet not rigid but rather fluid. Unlike Abrahamic religions which have clearly stated dos and donts and scriptures that in many cases form the law, Eastern religions have tended to be more ethereal. Dharmic religions belonging to Indospehere and Chinese/Japanese/Korean religions belonging to Sinosphere tend to deal with 'may/may nots' rather than Western religions that are more of 'can/can not'. The result has been an explosion of conflicting opinions, diverse cultural mores and habits that indicate a total lack of cohesion, but scratch the surface and you shall find layers and layers of similarity and commonness. Contrast this with western religions, where homogeneity is the norm.
When West met East, notably during the colonial era, West imposed its understanding of culture and society on the East. Manusmriti was understood by British colonizers as the Hindu equivalent of the Quran or the Talmud, which it certainly was not. Practices that the westerners found abhorrent, were termed as superstition (which in our understanding today, surely were superstitious). As Hindus became more prosperous and materialistic over a period of time, faith in Godmen and Seers and Saints dropped in this most religious corner of the world, Add to this the inherent fluidity of the religion to accept all views (even if they be diametrically opposite) has resulted in Hinduism being a religion practiced at home and thus varying from home to home. Barring a few recommended visits to famous temples and prayers at holy rivers, Hinduism is actually a way of life, and not so much a religion in the western sense.
India's independence and the Nehruvian belief in majority communalism being more dangerous further dented whatever consolidation could have happened amongst the right-wing Hindus that could have resulted in a rigidification/restructuring of the religion. Other than the failed Cow slaughter ban movement and the partially successful Ram Janmabhoomi Andolan, Hindus have remained a diffused and distributed lot. Combined with the inherent tolerance and respect for other cultures has meant that Hindus would be as likely to pray at a Pir Dargah as at Kashi Vishwanath temple. Given this political and social background, the Shankaracharya's rejection of Sai Baba goes against the grain of the religion which he claims to lead.
Which is a sentiment best summarized Rig Veda which says
'एकम् सत् विप्राः बहुधा वदन्ति'- Truth is One, though the Sages know it by many names!
