First of all, I agree with you that downvotes on questions that are fine after minor improvements should be avoided. It is better to close vote/flag instead and even better to edit to improve the question or help the asker do so with a constructive comment.
But I don't think trying to discourage people to downvote is the solution. I think it is better to acknowledge that looking for the best in posts that are usually rather poor requires a lot of patience, which not everyone can muster. This does not justify this behaviour, but it might explain it a bit. Also note that mistakes will happen even if everyone perfectly agrees, so there is no way to completely prevent these situations.
So, what can we do? I have a few ideas:
Provide more guidance to reviewers
Most of the questions vulnerable to being misunderstood appear in the first posts review queue. If anyone should 'protect' those who ask these questions it should be first posts reviewers. In this case 'protect' means to improve the quality of the post and/or be generally supportive of the asker.
Approaching reviewers can be done in multiple ways, we could make a meta post where we can point them to, mention in comments if they can improve or use chat for a more individual approach.
A lot questions seem to receive at most 3 upvotes during their active period. This means that one or two downvotes have a lot of impact on the post score. If questions receive more votes, the impact of 'bad' downvotes decreases.
The problem here of course is how to achieve this. However, it doesn't take many people to upvote questions. Maybe you (yes, you there, reading this) should upvote more?
This is just speculation, but one reason why people choose to downvote instead of flagging to close could be that questions do not get closed quickly. This means that, from their viewpoint, flagging has almost no effect even after waiting for a while, while close-votes have immediate effect.
Note that I could be wrong here and that questions put on hold are more likely to get more downvotes, but this is something we can consider.