The major issue appears to be the presence of perchlorate in the Martian soil. Perchlorate is an oxidizer that, as one blogger put it, "does bad things to organic molecules." Its presence, therefore, would reduce the number of building blocks for life.
http://www.wired.com/wiredscience/2008/08/report-mars-les/Since there are no microbes in Martian soil those would have to be shipped from Earth. Seems like they should rethink using martian soil. Hydroponics can use a medium like coco coir or plain old gravel pebbles, maybe that would be preferable.
Besides, hydroponics gives you absolute control of the ph level, nutrient level and minimize the possibility of bad soil microbes.
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