I agree that good answers shouldn't automatically be lost without the chance for human review. The Roomba doesn't delete in this case, so it's counter-intuitive that deleting a user does. Further, these auto-deletions don't even go to the 10k review page for deletions -- not that we should expect people to regularly review those anyway (the interface is poor), but even if they wanted to they couldn't. So that's no good.
I agree with your suggestion: it would be better to leave bad question with good answers in place (account deletion will anonymize them) than to delete them. We tell users clearly that once they post content they don't fully own it any more, so there is no reasonable expectation of question deletion with account deletion.
If leaving them undeleted is deemed to be too permissive, then we should apply human review instead of auto-deleting these.
For downvoted questions with upvoted answers, the system could leave the questions and raise an auto low-quality flag, sending the question to the review queue. Reviewers can then inspect the question in context and decide its fate. (The answers would also need to be presented.)
We already have auto-flags for low quality and users are used to sometimes seeing old stuff in the review queues, so adding this doesn't seem like it would surprise or confuse anybody.
Normally the options for questions in this queue are "close", "looks ok", and "edit". Closed questions do not go to this queue under normal circumstances, but with this change that could happen. For a closed question in the LQP review queue the "close" option should be replaced with "delete" or "recommend deletion", just like for answers. "Edit" (to fix the problem) + "looks ok" (post-edit) remains an option.
It's important that the answers be available when reviewing low-quality questions. I don't know if they are or not (I don't have an LQP test case at the moment). SOUP adds this for the close queue and might add it for LQP too.
Or if using low-quality reviews is too hard, we could at least raise moderator flags on deleted questions with upvoted answers. We now get moderators flags for some controversial reviews (I don't think we did back when I wrote this answer), which seems vaguely similar -- here's a thing on the site that requires human judgement, the processes available haven't produced a clear result, so mods should take a look. I'd rather see community review than moderator review, but I'd rather see moderator review than silent deletion like we have now.