There also are many tried and true ways to manage the heated water so that it is safe for the environment [1, 2].
"We pump that seawater through cooling modules - which are direct water to water heat exchange modules - and then the water is gravity fed from the cooling modules back out to a temporary building, which serves the purpose of mixing incoming seawater with outgoing return water, so when we return the water to the Gulf it is at a temperature more similar to the incoming water." [2].
I'm sure Microsoft was aware of all this before publishing their report. Good on them for thinking creatively.
[1]: http://www.datacenterjournal.com/industry-perspective-seawat...
[2]: http://www.datacenterdynamics.com/power-cooling/googles-finl...