So I tried 1.0.2. I couldn't really find anything to complain about at first. The heat gauges weren't even giving me memory issues, so I decided to leave them on and do a rather well-paying mission to retrieve a piece of debris from Minmus orbit. It was going fine until I was on a path to return to Kerbin, going straight towards the surface. Just after leaving Minmus' SOI, I realized it was probably a good idea to eject my final stage and fold up my solar panels and service bay, so I did it. After engaging time warp again, every part in my craft was severed from the cockpit, and there was an explosion. I quick loaded and tried again, this still happened. Eventually, I went to the tracking station to try time warp there. I waited until the craft was closer to Kerbin, and transferred to it. It was still in one piece, so I engaged timewarp one more time, thinking it was over. This time, the craft didn't explode, but it stayed in place above Kerbin instead. I could still see Kerbin turning beneath me. I let go of the debris I was carrying, and it slid off me and fell to Kerbin on its own just as it would as if I was hovering in place above it. This was especially odd since I had timewarp supposedly on. A few seconds later, my craft exploded just as it did before.
I quick loaded again, fell down to Kerbin without using timewarp. I landed without any problems and tried using timewarp on the surface. It behaved normally.
...is this a known issue? It's incredibly bizarre, and I did a couple other missions before this happened without any problems. If I'm going to have to deal with it again later, I'm probably just going to wait for a better bug fix which doesn't add more bugs.