There is a way to use smart way by using join:/ (in my case it was

[node:field-taxonomy-skolski:parents:join:/]

where "field-taxonomy-skolski" is a field for choosing term in taxonomy tree) Forward slash is stripped, though, but there is a setting in

Administration » Configuration » Search and metadata » URL aliases » URL aliases - settings

on the bottom of a page there is PUNCTATION drop-down. Set for slash (/) "no action" instead "remove".

There is a clever way to do this by using join:/

In my case, I used:

[node:field-taxonomy-skolski:parents:join:/]

where field-taxonomy-skolski is the field for choosing the term from the taxonomy tree. Forward slashes will be stripped, though there is a setting under

Administration » Configuration » Search and metadata » URL aliases » URL aliases - settings

at the bottom of the page for PUNCTUATION drop-down. Set to slash (/) "no action" instead of "remove".