Actualy it is reality. There are many people who do meet and get married at work, even where fraternization is frowned upon.My parents, my sister and her husband, and my husband's sister and her husband all met at work. That's where I met my husband also and we kept our relationship quiet and our behavior professional due to the non-fraternization policy along with other things, like not wanting to make others uncomfortable. I worked for a very large fortune 100 company and there were so many marriages. At one point we were considering putting all the couples on the cover of the annual report and say we were a "growing company."
I agree with Leola. It's interesting to hear how they deal with protocol and the crew and their responsibilties on the ship. I think it's more real than being stranded with someone you're attracted to for seven years and never acting on that attaction or addressing it at all. But all of that aside, I think it would have been great if during the last episode J/C disclosed that they had been together, since Janeway received the letter from Mark in Hunters, but kept their relationship discrete. That would have been awesome!
There is a difference between getting involved with a coworker and getting involved with your superior, particularly if that superior is your captain. That's nothing like getting involved with the guy/gal in the next cubicle...and it's not even a whole lot like getting involved with the guy/gal who has a slightly bigger office than you.
And as for "unrealistic," heck, as far as I'm concerned, and apparently as far as Janeway is concerned, if you're captain of the ship that's your priority. Is that unrealistic? No, I don't think so. Everything else has to take a distant second, even Chakotay. Of course it wouldn't be easy, and I probably couldn't do it because I personally think Chakotay is hot hot hot. That's one reason why I should never be a captain. A captain is supposed to have qualities that the rest of us don't have, and that includes the discipline to (almost always) put the needs of the crew ahead of your own needs. And in my experience (and I do have a little), really good military leaders DO have qualities that the rest of us don't have.
And I personally wouldn't think being lied to for several years, which is what your last scenario would have meant to the crew, would be "awesome," but hey, different strokes...