Did Morgulduin pollute the lower Anduin ?
 

The Morgulduin flowed from valley of Minas Morgul down to the Anduin below Osgiliath. Given the poisoned nature of the Morgulduin, did it pollute the whole of the lower Anduin ?

I would say no. The 'pollution' seems to be referring to some sort of enchantment or magic on the stream, and once out of the area of Minas Morgul, maybe the water would be safe again.
Perhaps a comparison could be made with the enchanted stream in Mirkwood. It flowed into the Forest River, which in turn went to the Long Lake and the River Running. The Lake-men apparently were not troubled by sudden urges to sleep.

Orcs gotta drink, don't they? Perhaps they had a higher tolerance for e-coli, dysentery, cholera and other waterborne diseases. Perhaps Tolkien was thinking of the Thames, which supposedly looked black and sorcerous until health reforms reduced dumping of human waste, animal offal and manufacturing slag over the last 100 years:

"The whole of the river was an opaque pale brown fluid...surely the river which flows for so many miles through London ought not to be allowed to become a fermenting sewer." -- Michael Faraday, The Times, 1855

'...a dank, stinking sludge, the scene of murders and crime'. -- Charles Dickens

That sounds more like what Sharkey's Men were trying to do in the Shire.

The Scouring of the Shire

What was going on in Morgul looks like something different, more of a spritual decay and corruption rather than a physical pollutant.

Even in Middle Earth, dilution is the solution...

If there was no magic, then yes, maybe, the river would be polluted out side of Mordor. But since magic exists I would be doubtful.