First time here and I just read through the whole thing. This is the best exalted crossover I have ever read, probably the best Highschool DXD crossover I have ever read, the best multicross I have ever read, and My favorite quest of all time. Moving on...
I don't think Serafall should join the harem, a one off tryst would be fine however.
The difficulty is doing so without compromising her personality and the complications that are involved with sleeping with such a powerful figure of the underworld. I think it is for the best if she and Ise don't become intimate, but them meeting is a must if only for their characters to bounce off each other, I want to see this Hammy, experienced, and slightly jaded Ise interacting with a Maou Shoujo (I probably butchered that pun). He will either take it all entirely in stride, and just nod along with the crazy person and try to limit the damage like he does with suika, or He will play along and they will become best friends as shonen hero and magical girl.
I also want to see that solution to the Mil-tan problem Ise mentioned (off handedly to kiba at one point) And what would happen to Mil-tan afterwords, would she join his faction, go off and do her own thing but stay in touch, join a different faction (cannon Serafall considered having mil-tan on her peerage because s/he is strong enough to beat magicians with just brute strength, imagine what s/he could do if turned into a typically overpowered magical girl (picture Nanoha's friendship beams but as punches, that is I hope the magical element of mil-tan's solution works with her current strength)).
Considering his new contacts (history compilation committe and the yokai) the spirit contract could done more safely, with his empowerement charm and study of both magic and the evil pieces, maybe bright sensei has seen a way to combine them- a ritual that substitutes his charm for the evil piece, and instead of changing the dna to make them related, use it to change the gender or something. Maybe he could just give Mil-tan the powerup and then help him develop a gender changing charm, like it said in shougo's interlude the half-caste charms are more personality based, a way to turn into a cut girl that is still really strong would fit Mil-tan's personality perfectly.