It's probably going to be for the better. My biggest concern though is that HN may become to clique-ish... Those with low karma that have interesting thoughts may now be discouraged from sharing...
I think you're doing the right thing. I've watched HN start to turn into a place full of snark and very useless comments. This is a great measure, but is the 1000 points karma a high threshold for the endorsers? Why not 500 or 750?