I don't think adding downvoting to submissions will mean HN==reddit, but a solution for those that think so: have "flag" display the number of times something has been flagged and have this negatively affect page rank similar to downvoting.
Benefits:
-Adds the positive aspects of downvoting as mentioned below: http://news.ycombinator.com/item?id=1366325
-Avoids downvoting submissions for mere disagreeance. Since the functionality is called "flag", rather than displayed as the complement to the upvoting action, it is explicitly only for objectable submissions and not because you simply disagree with something.
-Allows site to maintain status quo if moderators are busy/away. The site is self moderating.
-Allows better tools for moderators to solve problems quicker, for example they could filter submissions based on the ratio of flags to upvotes to see where their limited attention is needed.
-I don't think downvoting submissions with a karma prerequisite would be a major problem giving how well the comments system has worked. Set the karma requirement for flagging to same as comment downvoting could work.
-If you're still concerned about flag abuse of this new flag system, "flag (#)" would require the flagger to select a reason from a drop down-box of a limited lists of reasons that you decide are valid for flagging. This informs users of your desired direction for the community within an interface mechanic.
I think this is win win, it addresses the problem by simply expanding a current feature, but you probably have some ideas have your own in this area.