It doesn't matter if the super glue melts, as it's purpose isn't to hold the nut on permanently. It's simply there to hold the nut to the sump so you can stop whatever minor drips of oil might be coming out of the drain hole. Once the JB Weld cured, the super glue isn't necessary any more. As for the JB Weld, cured JB weld can withstand a constant temperature of 500 degrees, and a maximum temperature of 600 degrees for 10 minutes. The area around the sump isn't going to get anywhere near that hot.
If there was too much oil still dripping out for whatever reason and the super glue wouldn't adhere, I'd take a small piece of shop rag, ball it up, and then put it into the cut off corner of a freezer bag. Tie off the the end with some sturdy string, and leave it long enough so you can grab it. Stick that into the drain hole to block and remaining oil from dripping. Now you can clean the sump until it's sparkling, and then glue the nut onto the sump and continue. Thread the string through the nut so you can grab it. Once the JB Weld is applied and cured, pull the plug out of the drain hole and through the nut, and put the drain bolt in.
I've used JB Weld a lot in my fabrication projects. I've never done this specific type of repair. I suggested it mainly as an alternative to JB Welding the drain bolt into the sump than then having to use a pump through the oil filler port in order to drain the oil. It's not a repair I would do myself, as I'd opt for a Time Sert. But if I had to get the bike fixed and JB Weld was my only alternative, I'd try the method I described first. If it didn't work, then I'd just JB Weld the drain bolt in place and resign myself to pumping out my oil during oil changes. And I'd definitely try this method before I drained all the fluid out if the bike and layed the bike on it's side, or removed the engine.