Yep, there are a few transformative angles you can take.
First thing to note, is that it is unlikely that Richard Prince would sue. I guess that for the price tag, each print is unique. Why would he print twice the same thing when it takes him all of 10 minutes to find a decent image, screenshot it, print it and sign it (apparently for the Instagram copies, his comment is the signature, he doesn't even bother to sign) ? There is no loss of sales for him, and he's able to find suckers for his "unique" prints. Why would he risk losing a case ?
But in the hypothetical case... the courts say that an use is transformative (Firefox's spell checker doesn't like that word...) when it is "altering the original with new expression, meaning, or message".
About the expression, given that Suicide Girls have the original image, they could "reinterpret" the print by enhancing it with the original quality instead of the screenshot quality, and argue how it's adding depth, or adding contrast with the surrounding low-res text or whatever.
Or if it is about the context changing its meaning, at first it was an Instagram post, then it was a part of an art exhibition, then it is a re-appropriation for a charity. Hence I'm arguing that Mark Meyer's comment on how "While Prince’s use of Mooney’s photos adds new and significant context, Mooney is simply selling copies of Prince’s work with no additional contextual commentary" is wrong. In the end, the "context" is only about your capacity to convince that, really, "it isn't what it looks like". And Richard Prince is much more seasoned at that game than Mooney ever will.
About the message, I was thinking along the same line as you did. Something like, this is the actual message (the $90,000 / $90 poster), and the sold prints are only parts of the overall artwork, as so many parts of the message. With both Prince and Mooney, it's the same relation between the individual print and the "meaningful context" (art exhibition / re-appropriation for a charity).
However, I agree with Mark Meyer on that point, the "we added the "suicide girl true art" message" is probably not going to cut it.