limit exposed filter to top X taxonomy terms in drupal 7
I think the closest I have seen to doing what you ask is http://drupal.org/project/better_exposed_filters which tries to at least make the exposed filters more manageable.

EDIT:

If you are prepared to switch the filtering to faceted search you could use search_api module in combination with its built in facets (through solr). Then you end up with being able to restrict the amount of terms you show in the facet.