Yes, you should have no problem. Just tell any TMs who ask what you are doing and they should let you go.
FYI, if it's only the two of you and the main queue is too long for your taste, you could do the single rider and castle tour queues (one after the other) and you should not gave to wait long at all. The only major element you would miss from the main queue is the greenhouse area, which is no big thang, IMO.
ETA: Actually this works even if there's more than the two of you. You will be split up in different ride vehicles, but that doesn't matter much on FJ.