I can say only one difference with these two.
It is based on Joomla api version. JUtility::getToken()
is available from Joomla 1.5 and
JSession::getFormToken
available from Joomla 1.6.
In fact both are doing same task like here and this.
So may be in future JUtility::getToken()
may be depreciated or removed from latest versions like what Joomla did for DS
constant Its available from J1.5
to J2.5
but on J3.x
Its removed and they use DIRECTORY_SEPARATOR.