This is not a great workaround, but it's better to debug in assembly than not to debug at all:
1. Compile your code as usual into .elf, .hex, and (optionally) .eep
2. Strip all extra section code from the .elf with:
$ avr-objcopy.exe -R .sect1 -R .sect2 code.elf code.elf
(The above assumes your file is code.elf and your bootloader sections are .sect1 and .sect2. You'll have to tweak this to suit your needs.)
Do not delete your .text section.
3. In Studio 4, select "Select Platform and Device..." from the Debug menu.
4. Select your ICE and check the "Open platform options" box
5. Autoconnect and start auto-programming to burn the .hex and .eep into your AVR.
6. Start debugging
7. Studio will pop up a dialog box. Set your clock frequency and on the Debug pane, select "Don't reprogram device"
With luck, Studio will NOT crash and you will be debugging your actual code (since you've already loaded it from the .hex and .eep files). The downside of this approach is that you will have no debugging information in your added sections, but like I said, debugging those bits in assembly is better than not debugging it at all.