It sounds as if perhaps Sam wants to talk with you about his decision to change and is seeking your support for that, while Sue wants to talk about how badly hurt she is (and possibly about the fact she might want to leave Sam, is that where this is going?). Is that correct?
If that's the case, it's really the same fundamental issue as with any couple even without the transgender aspect involved: Two halves of a couple are trying to bounce very different perspectives and emotions off the same person, in this case, you.
Being a sounding board for one person is doable. Being a sounding board for both halves in ANY kind of relationship is unwise; it puts you in the middle; it puts you in possession of information about each of them that the other might want to know. And if even if they'd never dream of asking you "What did Sue say about her feelings?" or "What did Sam say about his plans for him and me?" etc. -- you really should not be put into the position where that could even remotely happen.
I think maybe you're somehow worried that if you tell either or both of them that you don't want to be a sounding board, you might be perceived as being anti-transgender by Sam and other friends, or as being mean or cold in Sue's eyes. But please don't worry about those perceptions; YOU know they wouldn't be accurate. You know you're OK with his choice and at the same time you're feeling compassion for Sue.
Just do what you have been doing: "I really do hope this goes well for you, but I have to be honest, Sam, that Sue has also wanted to talk about things, and I am not comfortable being the sounding board for both halves of a couple I really like and value. That's why I'm glad that counseling is part of the plan for your transition, because I'm not qualified to help and I wouldn't want to say things that would hurt either of you." You can say the same to Sue.
You are being sensitive and at the same time recognizing that you should not step in where professionals are needed for both of them. The one thing you might want to tell Sue is that since Sam has to get professional counseling as part of his transition, she, too, should seek out counseling or therapy to help her figure out what happens next for her.
It has to be tough to decide how and when to see them together as a couple if you are not sure how long they will continue to be a couple. But for now, I'd keep inviting them to whatever kinds of things you did with them before Sam shared his news, and let them take the lead on deciding what invitations to accept or reject. Don't cut off contact; just continue treating them as the couple they are, until you hear otherwise from them.