If HL3 is using some modified version of the source engine, most of the programming work is done already. Most of the tools and functionality required exists already. The game is most likely stuck in artist/design land. Even if Greenlight's development diverted attention from HL3 it serves us way better than HL3 ever will. We will get more games, as valve no longer has to accept games manually. Even more than that we will get more 'cheap' games because this system will push more indie titles onto steam.
It could also push shitty games onto steam if there isn't some secondary approving or denying process. I look forward to seeing how it works.