I've been running 1.0.5 until now, and my game always crashed at the end of a simulation anyway. I don't think it's a bug, just the sheer volume of mods I run. In career I just deal with it and reload (SSD ftw) because of the sim costs, but most of the time I play in science mode and have found a better way that doesn't require yet another mod.
I just use a Sandbox save literally called 'test'. I copy the .craft files from my actual save to that, build and warp until done, launch, and record problems and revision ideas on a piece of paper. You can also quicksave and use notepad++ to edit the ship into various orbits, which is a simple thing to do and useful for testing rovers, landers, and ships you will be building in orbit (so you can make sure they work first, then worry about getting them there).