These and similar issues have been discussed before as important bugs to fix. As part of a conversation with the Catalan Community some of them were identified as must-fix issues before exposing the tool out of beta, but it is the first time that they are presented as an urgent situation for the tool to be disabled even as a beta feature. So I'll try to provide my point of view, and ask for some additional information that can help to better understand the impact of those problems.
Our understanding has been so far that most of the time the users that created the translation where the ones having to fix the issues in the markup the tool produced. This means that if they are still using the tool to create those articles, it is because the benefits of the tool compensate the usual glitches of a tool in active development.
Another important consideration is that Content Translation is mainly used to create new content that did not existed before (the tool discourages overwriting existing articles). So no harm is expected for existing articles. Please, let us know if you find otherwise.
In addition, we expected that when the articles don't meet the quality standards of a wiki, they will be deleted. We are tracking deletion rates as a way to estimate the number of low-quality articles and they are quite low (about 8%). The problem you are raising (articles with content good enough to keep but with a markup that requires effort to fix) is harder to track; is there a way we can estimate the number of articles that create heavy clean up work for other editors?
Wherever we see that inappropriate content is added to generated wiki text, we are quickly fixing them and deploying the fixes every week. So the tool is rapidly improving on that aspect. For example we are deploying https://gerrit.wikimedia.org/r/229313, https://gerrit.wikimedia.org/r/229106, https://gerrit.wikimedia.org/r/228242 and https://gerrit.wikimedia.org/r/228773 on this Thursday to address these kind of issues.
We estimated the general overhead for communities to be low since the tool is exposed to few users through the beta feature system (and those tend to be experienced users normally). For Catalan Wikipedia (which is the wiki with more articles created with Content Translation) there are 15 new articles translated per day. That wiki has about 100 new articles per day, so Content Translation represent a small fraction of the articles produced which we assumed not to represent a heavy workload (if you consider that only a percentage of those may have issues not fixed by the article creator). For English Wikipedia, Content Translation is generating 10 articles per day (out of about 1000 new articles), with much more active editors.
The tool is already useful for many users, and great articles have been created with it. Thus, if we disable the tool we will prevent these users to create great content with it too. Interrupting the service would be a really major measure and while we do not want it to cause disruptions as pointed out in your comments, we would like to work towards cleaning up these issues on a priority as they are discovered. There is a counter dependency here for which we appreciate the feedback we get from the community as the one you provided.
We have been trying to interact as much as possible to compile examples of the issues that are causing impact (good and bad) and it is important that we can get a better picture of how they are affecting different people in the different communities to identify next steps. Feel free to use this discussion page or Phabricator for adding further details on these kind of issues.