Is there a difference between government establishment of a religion and the freedom to worship?

Yes, there is a difference between these
two.

Government establishment of a religion has to do with
the government telling people that they must participate in religion in some way.  This
is what courts ruled the government was doing when schools had school-sponsored prayers
as they did decades ago.  In such a case, the government is, arguably, setting up (or
moving towards setting up) an official religion.  The establishment clause is taken to
prevent the government from taking such positive actions to
compel certain religious obersvances.

By contrast, the
freedom to worship is negative.  In other words, it
protects people from government efforts to prevent them from religious observance.  In
the public schools, for example, this right ensures that students can engage in prayer
or other religious activity so long as it is not disruptive.  That is why a school could
not ban students from doing the "prayer at the flagpole" type of things that some groups
engage in before school.