How to disagree about author order when my advisor has been dismissive of such concerns in the past? I'm being asked by my advisor to perform a specific scientific experiment that she conceived from start to finish  on our apparatus over the next two months (which could easily become 3-4 months or even longer).  There is a senior graduate student, but he is writing his dissertation.  The advisor has asked me to run the lab 45 hours per week to take data on this experiment.  The advisor has told me that the senior graduate student will provide some guidance and we will work together on a conceptual level, but that I will do all of the day-to-day setup and data taking.  So far, the senior graduate student has only acted as a buffer of communication between the advisor and myself, and he has simply passed on parameters for me to test that were suggested by the advisor.  

The advisor has indicated that she wants the senior graduate student be the first author.  I believe that this is only because the senior graduate student has not published a satisfactory number of papers and must graduate this semester (he is a 7th year graduate student).

In the past when I've questioned the ethics of authorship on papers, particularly pertaining to this exact scenario, my questions have been brushed off and I've been told that this is how it has been done in the past in our research group: a junior graduate student will take a lot of experimental data for the senior graduate student.  To call myself a junior graduate student may be misleading, I am in the fifth year my PhD program and I have not yet started my independent research in the lab because I have been taking data for the previous graduate student for several years now.  I fully have the expertise to run this new experiment without any input from the senior graduate student.

It seems to me that, simply questioning my advisor's ethics with regard to how she assigns responsibility and authorship in the lab, has run into a brick wall.  It has made things awkward and has not changed anything.  

I want to consult other professors but I fear that their conception of authorship is just as corrupt.  I would also like to speak to our dean but I fear that word will get out and it could come  back to hurt me a later point in time.

How have people dealt with this in past?  It seems that there are no definite guides for how to determine authorship in such specific cases, and I feel that my advisor is abusing the undefinitive nature of authorship ethics!
Depending on your field, it may be possible to submit your paper to a journal which allows for "co-equal first authors": that is, both the first and second are treated equally as first authors within the journal. You could then mention this in your CV. That way, I don't think there's much harm done; this would represent the path of least resistance.

Otherwise, you're going to have to be willing to involve someone to deal with this issue—whether it's your advisor, the dean, or other professors in the department. There's no way to resolve this issue without it. (I presume you mean the chair of your department, or other similar official, when you use the term "dean.") But the first step should be to talk with your advisor, before the paper is written. You may be able to clarify things at that stage. I'd involve the other members of your thesis committee (if you have one), and then finally work with the dean.