Is there a way for me, while debugging, to mangle the symbol table to remove Foo::Bar::Baz::AUTOLOAD subroutine?

You should be able to redefine the subroutine by assigning a code reference to the appropriate glob.

*Foo::Bar::Baz::AUTOLOAD = sub { 1 };
[download]

I'd assume that you can make that happen in the debugger by typing it in as an expression. For example, see this debugger session I just tried:

(0) $ perl -de 1

Loading DB routines from perl5db.pl version 1.28
Editor support available.

Enter h or `h h' for help, or `man perldebug' for more help.

main::(-e:1):   1
  DB<1> *main::AUTOLOAD = sub { print "$main::AUTOLOAD @_" }

  DB<2> main->foo(1,2,3)
main::foo main 1 2 3
  DB<3>
[download]

You could probably even save the original AUTOLOAD code reference to a new, lexical variable, and use it to call the original AUTOLOAD in your replacement after filtering out calls to DESTROY -- that would hopefully keep the rest of the code working, too, if that was important.