Thanks for the suggestions. I agree that improvements should be made to the interface, but I myself can't do anything about this for awhile because Ruth Chabay and I are currently consumed preparing the fourth edition of our Matter & Interactions textbook.
At the risk of stating the crushingly obvious, there are workarounds available for some of these issues. When you're not editing or running a program but rather looking at the contents of a folder, the bold-face "GlowScript" at the top of the page does take you to
glowscript.org without signing you out. Another convenience is to open another browser tab and go to
glowscript.org in that tab, which you can keep around. You can generally get out of traps by clicking the "Replot" icon of your browser. That for example makes it possible to use alert again. You might also consider using print rather than alert, or console.log (see Work with 3D objects > Text output). To rename or move, just copy the program text, create a new program, paste in your text, and delete the old program.