A couple things from the article.
"By law, any graves more than 75 years old can be removed. "
That seems to be something fairly easy to either understand or change if that is the desire of the majority of folks in the area.
"The City of London and Tower Hamlets Cemetery was opened in 1841 by an Act of Parliament. "
and
"Other markers have gone altogether, torn down when the graveyard was deconsecrated as a Church of England cemetery by another Act of Parliament in 1966 when it was deemed to be full.
The intention was to create an open space for the public, which led to two bomb-damaged chapels being demolished and a swathe of graves cleared.
In 1986 ownership passed from the Greater London Council to Tower Hamlets and in 1990 the Friends of the Tower Hamlets Cemetery Park was set up.
Seven years ago the park became the borough's first nature reserve and it is now tended by 1,600 volunteers."
There is ample precedent for the change. It just seems to be an issue now because of the muslim influence in the change proposed. It's pretty obvious that there have been changes in the cemetery's status previously so I doubt there is really any true reason to block the next change. The slant on the story does make for a nice sensational or tabloid effect though.
It will be interesting to see what they do with the remains when they dig up the graves. It seems a shame to see a bit of history go away, but I don't see anything that will prohibit the operation.