I thought I might write an update on this in case anyone else is interested...
The answer is yes, we can break E6 (to anything) while maintaining spacetime SUSY. Models with E6 are known as (2,2) and models without E6 as (0,2). (0,2) means N=0 Superconformal symmetry on the the left-moving sector on the worldsheet and N=2 Superconformal symmetry on the right-moving sector on the worldsheet. There is a big literature on (0,2) models but the important information is that they do indeed have spacetime SUSY. In fact, a theorem in this paper states that N=1 spacetime SUSY requires (at least) (0,2) worldsheet SUSY.
The take home message is that E6 gauge symmetry on the bosonic sector corresponds to N=2 Superconformal symmetry on the worldsheet.
This post imported from StackExchange Physics at 2014-03-31 16:00 (UCT), posted by SE-user Heterotic