I'm being elliptic about why here because I don't think I can talk about the internal architecture of that system in public, but warning people off one particularly stupid third party bug that we fixed in our internal fork is not, I believe, a problem. Anyway, we certainly did use it to manage daemon processes, although not deliberately; we had a daemon that communicated with external software about system events, and running shell scripts was part of that. We didn't necessarily anticipate folks running 'service httpd start' in those shell scripts, but it was not an inherently unreasonable thing to do.
And this isn't "arbitrary use cases"; this is an explicitly supported function that is completely contrary to good practice and sane behavior and, to boot, has the ability to arbitrarily kill programs for impenetrable reasons and block for significant periods of time (the central sin of event driver programming). You can't tell me that if you saw something like this in a random crypto library you wouldn't immediately tell everybody to stop using it; why should EM's developers get a pass for their, yes, incompetently written popen? I would actually be considerably happier if it wasn't in the library at all; at least then it wouldn't be wrong.