There are many TS restaurants that I have browsed the menu for and would LOVE to have an app or desert from, but have always felt uncomfortable/fearful of going to just for one thing. Is this acceptable? Really? Do they get mad?
None of them really care if you order small plates/apps or just dessert, and if the servers do care they certainly won't show it. And if they do, just ignore them or ask for management or a re-seat. (I've never had problems in this situation, and I do it on a fairly regular basis because I like apps in some of the places where I don't particularly like anything else on the menu lol.) I personally wouldn't book one at a peak meal time (i.e., between 6 and 8pm when dinner rush is in effect) but that is just to give the servers a chance to have full-meal tables for dinner and deal with my small-order table during a slower time period.
Will most TS places let you get a app or desert to go? Can you just order from the Check in kiosk?
Very few TS handle to-go. They certainly aren't set up to order/pick up like regular non-WDW restaurants may be. Very few of them even have containers they could put your food in. To-go desserts could be had from one of the numerous bakeries in parks and resorts without anytone blinking an eye, but TS apps/desserts to go are less do-able. Some restaurants will try to accomodate you if they can, but expect to wait and be ready for a bit of confusion from the staff. The check-in folks have a computer system which allows them to handle reservations and seating, and to enter your information when they check you in to pre-program your tab/ticket and streamline the server's job inside - but they are not set up to take orders or money.
For example, I have always wanted to try the chicken bastilla from Marrakesh in Epcot. Can I get this to go without sitting for a whole meal? Or is that just rude?
Theyre so good! 
