I've had some instructors that spend more time out of the saddle than others. I like being out of the saddle, so it doesn't bother me one way or another. I will sit down or stand up as needed, regardless of what the instructor is suggesting we do. Assuming proper form, getting out of the saddle works muscles that I want to work, regardless of whether it mimics what I actually do on the bike on a regular basis.
I think Dogmamma touches on some good points. While many of us turn to spinning, especially in the colder months, to get a "cycling" workout, spinning is first and foremost an aerobic workout. Not all of it does, or necessarily should, mimic cycling in real life. It's similar but not identical.
IMO, if something doesn't feel good, then don't do it, but I wouldn't assume that something in a spin class was contraindicated just because I couldn't do it for the length of time suggested by the instructor. Even when I've in great "cycling shape," at the end of the season, a good spin class will usually kick my butt.
Live with intention. Walk to the edge. Listen hard. Practice wellness. Play with abandon. Laugh. Choose with no regret. Continue to learn. Appreciate your friends. Do what you love. Live as if this is all there is.
--Mary Anne Radmacher