I like when hosts are actively looking for security issues. Most hosts are Negligent, hosts should not “leave security to their customers”, security is too complex and too important. If your host’s attitude to security is “we don’t support third-party software”, Leave Them. GoDaddy Managed WordPress hosting is not the best on some things, but they are at least Trying to keep your site safe.
Having a plugin disabled is inconvenient. But not nearly as inconvenient, and not nearly as hard to fix, as when your site gets hacked because that plugin wasn’t disabled.
(Keep your eyes open for updates, in case GoDaddy found a vulnerability and the author fixed it.)
Notice the Ninja Forms change log, they are finding and fixing potential security problems. Sign of a good, professional programmer.