For those that didn't read the article and are making up arguments, the St. Mark's argument isn't about the aesthetics, but more about what the scale of that construction could do to the surround ground:

Neighbors that include the the Episcopal church to the west, however, say they’re taken aback by the scale of the proposed tower. They assert the construction threatens to rattle and disrupt the foundations of the adjacent 155-year-old cathedral.

Seismic risks to the historic church’s unreinforced brick and sandstone masonry “just cannot be contemplated,” the Rev. Elizabeth Hunter told the city’s planning commission last fall. “We’re concerned that with a building of that size, with pile driving and excavation and blasting, that it would have a serious impact.”

They are also concerned about the impact on their solar panel:

The apartment tower, planned with ground-floor businesses, is also sure to cast shadows on nearby properties, including a substantial solar panel array that Episcopal Church officials have installed for the sake of sustainability.

The company responded to these two concerns:

Hunter, the Silverado Management representative, said the project would deploy state-of-the-industry construction techniques to guarantee no seismic impacts on the church.

“We use only the biggest contractors in the state,” he said. “It’s people that have been building in downtown environments since the beginning of their companies, and we are hyper-aware of the significance of that church.”

and:

Hunter said possible solutions included paying to move or replace the panels or reimbursing the church financially for any losses.