Note:  This post is meant for all aspiring fanfic writers.  Rachel's
question just made me think of it.  These are all my opinions, feel free
to disagree with any of them.

You can really do what ever you want with the charaters - as long as you
are able to give us a plausible explanation as to how it happened. 

Generally how I work is I ask a question to get me started on the fanfic. 
Let's take Rachel's question about Tim as an example.  Would Tim have the
guts to releave Hudson, Ford and Kimura from the chain of command?

Now that I have asked the question, I have to decide what the answer is.
In Rachel's case, Tim he is a UEO officer, so theoretically he knows under
what situation relief of command is acceptable.  So it is possible.  But
it would not be easy for Tim, for a variety of reasons. 

Now I look at how answering the question will affect the characters
involved.  You have to remember that it is the characters that are the
most important thing in Fanfic.  If you gloss over things, you are not
doing yourself any favours.  In fact you are hurting your story.

So how does Rachel's question affect the character involved:

*Hudson - Tim is intimidated by this man.  So to releave him of command
would be a tough thing.  Hudson does not strike me as a man would give up
easily.  Tim would have to find his backbone, and quickly. If Hudson
needed to be relieved, he isn't going to listen to cool logic. 

*Ford - This would be a gut wrenching thing for Tim to do.  He and Ford
are the only plankholders left on seaQuest.  They've known each other a
long time, and have been through a lot together.  They respect and trust
each other.  Ford would probably still listen to reason (even in Lostland
he was cool - as Bridger said this guy could do a crosword puzzle in
a plane crash) and step down upon Tim's suggestion.  But it would still
not be an easy thing for Tim to do.

*Kimura - This would also be very difficult for Tim to do.  This
woman used him like a piece of Kleenex.  So there would be a question in
everyone's mind "Is he doing this out of spite?"  Of course you could
argue that despite the fact she has the rank of Lt. Commander, would she
be in the chain of command.  If the answer is no, then you have already
solved the problem

*The rest of the crew - these people are just as important to the story as
the main characters.  It is important to remember that a commander is only
as strong as their team.  If the crew chooses to support Tim in the
removal of the officers - then he would have less problems.  If the crew
chooses not to support Tim - then that would open a whole new set of problems.

*Tim - This is the most important character in this story.  We as the
reader have to not only know why he made the decisions he did, but how he
got there.  Let the reader spend time in Tim's thoughts, hering him go
back and forth between should he or shouldn't he.  We know that this would
not be an easy decision for Tim to make.  Show us how difficult it is.

Now that we have figured out how the characters would react to the
question/ansewer/situation, the next step (at least for me) is the laying
out of the plot.  How do we get from the question to the answer.  For me,
sometimes this just flows out, other times it is like pulling teeth.

Once you have the plot, then you can write.  And in your writing, you
discover that certain parts fly out of you, others just don't seem to
come.  You also discover that what you had perfectly worked out in the
plot isn't going to happen that way.  The characters are taking you
somewhere else or you have had a flash of brilliance.  You have to be
flexible.

Then comes editing.  This is the trickiest stage as we have to choose what
scenes to keep and what to ditch.  Scenes that we originally believed were
hillarious/deep/brilliant may not fit, and they end up getting dropped.  
And it is in the read trough that you find places that don't really work. 
Maybe they need to be expanded, maybe pared down, maybe (the hardest one
of all) they need to be taken out completely.  I know I repeated myself
here, but it is an important thing to remember - You can't do everything
in one story.

Having done that I recommend sending it to a friend or two to read it
over.  There are five people who read *all* of my stories.  And without
their help, I would be nowhere as a fanfic writer.  When they are done,
take their suggestions and see if they work.  You can ignore some of what
they recommend, if it doesn't fit the story.  Then give it another read
through, just to make sure you haven't missed anything.

In short:  It is our job as a fanfic writer to do strange things with
these characters.  Things that the television show wouldn't do with
them.  What I recommend is that instead of asking "Is it possible?"  ask
"How would it happen?"  Trust yourself to find the answer.