The "date" command found on ESXi is not the same as your normal GNU date command, it's from Busybox.
However, you could get use python to get higher precision.
#!/bin/python
import time
print "%.20f" % time.time()
~ # date +%s
1341218714
~ # ./getTime.py
1341218718.30932903289794921875
Just out of curiosity, what type of experiments are you doing within the ESXi Shell that has these requirements?