Taxonomy terms are attached to nodes using term reference fields in Drupal 7. As such, you have access to the term reference field just like any other in the list of replacement tokens.
Look for fields related to the node with a description of "Term reference field", e.g.
EDIT:
To address your edit, I know it looks ridiculous but something like this will probably work (using field_school
as an example):
[node:field_schoolfield-school:vocabulary]/[node:field_schoolfield-school:parent:parent:name]/[node:field_schoolfield-school:parent:name]/[node:field_schoolfield-school:name]
Here's another screenshot showing the extra data available for term reference fields in pathauto: