But just telling someone the answer might be available somewhere else doesn't direct future traffic to the canonical question, which is the entire point of the "marked as duplicate" flag. If your question gets marked as duplicate and the question it's a duplicate of is a different question, it is not very hard to get it "re-opened". Maybe people don't know that this is true, but I think the main people having problems with questions marked as duplicates are new users where you've had very little time to educate them about what it means to have your question marked as a duplicate (basically, not much). Even if you made the "marked as duplicate" flag less obtrusive or whatever, politely saying, "Your question may have an answer at <url>" probably will get interpreted as "RTFM", and called user-hostile as well.
As an aside, my only experience with having a question marked as a duplicate happened on a sister SE site - it was my first post there, I asked a question, then after posting I found the answer in one of the "related questions" links on the sidebar. I answered my own question with a link to the other question and a description of the answer I found there, then flagged my own post as a duplicate. Both the question and answer were highly upvoted.
I don't disagree with that assessment, per se, but I don't think much can be done about it. The message doesn't say, "Fuck off, you worthless loser", it says (taken from the site), "This question has been asked before and already has an answer. If those answers do not fully address your question, please edit this question to explain how it is different or ask a new question." The fact that you interpret this as "fuck off" more or less proves my point that anything hinting at, "Maybe the answer can be found here" will be interpreted by new users as "fuck off".
I suspect it would be difficult to (automatically) distinguish between instances where a user was discouraged by the message and instances where the user's question was answered at the link. Perhaps the fraction of instances where the question was edited after being marked as a duplicate, then re-opened, is an OK metric for how willing a given community is to re-open questions.
As an aside, my only experience with having a question marked as a duplicate happened on a sister SE site - it was my first post there, I asked a question, then after posting I found the answer in one of the "related questions" links on the sidebar. I answered my own question with a link to the other question and a description of the answer I found there, then flagged my own post as a duplicate. Both the question and answer were highly upvoted.