Thread.interrupt seems to stop repository

We have a sporadic problem with Sling's JCR installer 3.3.8 and Oak (tar mk). It seems to timing related: the JCR installer does a Thread#interrupt at one point and sometimes this brings the hole instance to stop. Nothing else is going on any more.
While of course, a workaround is to remove the Thread.interrupt call in the JCR installer (which we did, see SLING-4477), I have the fear that this can happen with any code that is using the repository and gets interrupted.
This error is hard to reproduce, however with three people testing we could see this several times happening