Sorry to hear about your unfortunate experience OP.
With regards to the check-in and pre-departure stuff, delays at check-in are unfortunate but sometimes unavoidable, no matter your class of service - I think that is just bad luck, and nothing really to get stressed about as you still made the flight, even though 15-20 minutes is valuable lounge time! As regards to champagne and nuts for pre-departure, I am unaware of any airline that offers more than that for J class travel...there should have been a hot towel though!
However, I would be more concerned with the substance of your complaint, which is the special meal request. Assuming you requested a special meal specifically over the phone or via Manage My Booking (there will be note on the manifest saying GFML) - then you will have received, before main meal service, a separate meal with a big sticker saying "Gluten-Free meal". In economy, they are quite substantial (well, at least for Y food on airlines) - the portions provided are similar to the portions for normal meals. In J it is the same thing.
If you had requested this and they confirmed they had it in the booking and not loaded it on board, I would follow up with Emirates via the usual complaint channels because that is not acceptable.
However, if you had just mentioned your gluten allergy in passing or in a generic email to them without them confirming that they had booked a special meal for you (as opposed to them saying, special meals were
available) - I appreciate there may have been a miscommunication with EK staff on the phone - then unfortunately there would be nothing available for you on the plane. You can't mention it at check-in either, as it usually takes 24-48 hours to process such things depending on station.
DYKWIA: judging by some of the trip reports and posts about EK F&B, ground and air, is there such a thing as glutton free meals on board?
