Well, Warhammers are UEF torps so they should be friendly. However they shouldn't ever be hitting the Rheza, I guess they're launched by the Vatican at the nearby Deimos but somehow missing?
After some testing I can confirm that the mission is ****ed up, the Rheza kill is being credited to Omega 2, a friendly Uriel. Actually, it looks like the entire damn Uriel wing is hitting Rheza for whatever reason. Since the mission itself hasn't changed for over 3 years(and it was totally doable back then) this must be due to an engine change. I'll look into it a bit more and report back.