I think it's good that the system does this, and I don't think it should be more difficult for questions to be deleted automatically.
I think that what happened in Franck Dernoncourt's case is terrible and I really hope that it gets sorted out quickly. But I think that case is exceptional, and should not be considered a flaw in the system, but rather a case of one person behaving maliciously, which is something that hopefully moderators can deal with.
Since traffic is rather high on Ask Ubuntu, most questions don't get enough attention. Reasonable questions do get missed because they require knowledge that relatively few members of the community have. In general, maybe we should be a little bit more generous with votes on questions; as You can vote - do it! suggests, I think we (the whole community) should be voting more - if a question appears to have value, then please consider upvoting it, to help attract some attention to it.
On the other hand, if a question is of poor quality, sometimes it will get closed and sometimes it will just get ignored. Requiring -3 to delete a question would make it very unlikely that poor questions would ever get deleted, because very few attract so much negative attention (I do some cleanup, and I find a lot of bad, unanswerable questions with no votes either way - further to what I said about upvoting in the previous paragraph, please consider downvoting questions if warranted too!) and poor quality unanswered questions are just a dead end in search, bringing down the overall usefulness of the site.
In those cases where a question gets a downvote that causes it to be deleted, the asker is free to ask the question again if they are still having the same problem. New questions have a much better chance of being answered than old ones. Franck Dernoncourt pointed out in his answer that users are not notified when their questions are deleted. I think it would be better if users were notified in that case, so that they could take action.