I personally would have her go through the line with you and then chicken exit, rather than spend the entire time waiting without you in a gift shop or something.
Just tell the cast member as you are loading that she has decided not to ride (heck, maybe being in line she will decide TO ride) and she can wait along the exit path for you.
(I do this for pretty much every ride, since I cannot ride rollercoasters due to a neck injury. But it is more fun to wait in line with friends/family then to wait outside of the lines by myself.)
If it was more than just the two of you, going to do an alternate activity might be more fun, but since it is just the two, have her chicken exit. For rides that load and unload at the same place, you can usually just walk over the seat and wait on the other side of the platform. Just tell/ask the cast member so they know how to load the cars properly.