It seems to me that the MIF route can contain anything in terms of actions, from covert operations and gaining trust to obtain information, to creating your own "Manchurian candidate" and using it to destroy several key individuals, which will give neighboring countries a key advantage during an attack and as a result of the destruction or significant weakening of the Empire and as a result of improving the lives of not bound man.
In any case, it will dilute the usual romantic lines.
Yeah, but it'd require the devs to go "all the way". Spit-balling here, but, IIRC, there's a secret facility underneath the Temple (which could, potentially, house crimes-against-humanity grade experiments), so maybe the MIF handler of the MC could recruit him into weaseling into the good graces (by being an absolute slut) of Claudia, or Mallory, or ,even, Dr. Dykstra, getting access, collecting evidence and then giving said evidence to the handler, so they could pass it up the chain to their superiors. That could result in international condemnation of the Empire or even flat-out military action. However, the MIF are more of a freedom-fighter faction rather than an intelligence agency, so it'd be hardly believable and immersion breaking.
Thus, I'd suggest this - outsider futa (because how else are you going to infiltrate the Empire without being closely watched) who is really a spy, SEDUCES (Wow, I know!) the MC instead of bullying him into helping her gain the intel she needs to catch the Futa Empire by the balls. The Temple gets declared a terrorist organization and all its members are imprisoned, made to wear chastity or some other malarkey. A little cliche, but could be pretty ripe with intrigue and sexytimes.
There are already three characters (four, if you count Claudia, because she's banging Demetria) associated with the Temple, so finally, all those "Affection points" could be used for something else. Gain full affection of each character, then backstab 'em. Spy shit. Since there's already routes to gain affection for those particular characters (could count Suni affection for Dr. Dykstra), only thing left is do a beginning and ending for the Spy. 'Course, there oughta be some lore for some other country or alliance of countries strong enough to stand up to the Empire. Albeit coming up with shite like that oughtn't be difficult.
TL;DR: Sexy, seductive spy Futa from outside of Empire instead of MIF sounds better.