Because you can't warn for a tornado hours out, and even with higher tornado probabilities, it's no guarantee you'll even get a shower, much less a direct hit by a tornado. Just look at the huge area, that still only had a 10% chance of a strong tornado within 25 miles of a given point:
http://www.spc.noaa.gov/products/outlook/archive/2013/day1probotlk_20130520_1200_torn_prt.gif
Tornadoes are just too unpredictable to make far-reaching decisions like this. Think about all the other schools that didn't even get a little wind, but were under the same probabilities of the school that did get hit.
That said, the school likely had minutes, maybe as little as one to get to cover. I'm thinking they had at least 6-8 given that they were able to get the students into the hallways, but even that's not very much. I hope that this disaster strengthens the need to continue researching tornadoes in the hope of providing better warning times.