So, with the grief nanoparticles achieved, we have successfully figured out how to do the "trench coat billowing in the wind as we make a Clear Seed" trick!
Also, Kyubey was very forthcoming and helpful. I say we reciprocate that (within reason)--a helpful, cooperative Kyubey is VASTLY preferable to one that is antagonistic or quietly hostile.
I think Kyubey views Sabrina as a potentially huge payoff for the system as a whole, to an even bigger degree than contracting Madoka. Because Sabrina is not only completely unique and unprecedented in multiple ways (her strange soul, her power--which is all about controlling something that the Incubators consider to be a magical energy source, etc.), she has the potential to lead to new discoveries that could reform the whole system for greater efficiency/efficacy across the whole. In a past loop, Kyubey considered Madoka Witching out to be simply fulfilling Earth's energy quota considerably early--a blip on the radar, at most. It's possible that, in Kyubey's eyes, Sabrina has the potential to improve the radar itself.
Thus, we have a lot to gain by establishing a cooperative relationship with Kyubey. Yes, there is the obvious trauma involved for Mami, but we should be able to keep the two separate without any deception involved. So long as we're cooperative (within reason, which is easy--Kyubey hasn't even really objected to our plans to distribute Clear Seeds, for example), he should abide by any request to not bother Mami or show up whenever she's around. We could tell Mami--truthfully--that we're willing to be cooperative with Kyubey for mutual benefit, even if we know that he has no intention of actually being anyone's friend. A purely business relationship, in other words.
Also, we should definitely ask Kyubey to get us in touch with Kuroki Matsuko. For one, he just confirmed that she's still alive, which is a surprise (the latter part, I mean). We don't know how long she'll stay that way, though, and we should make it a priority to check up on her and provide aid if she needs it.