This sounds like you may be using DSpace 6 or an earlier version of DSpace. This issue was fixed in DSpace 7.0 (and any later releases) and it's now possible to delete EPersons even if they are referenced elsewhere in the system. This was fixed in
https://github.com/DSpace/DSpace/pull/2229
In DSpace 6 or earlier, you may be blocked from deleting these referenced accounts. You may want to instead clear out all the user information in that EPerson object (leaving a fake/empty object). Others may have other suggestions of ways around this, or you could upgrade to DSpace 7.x.
Tim