How do I build two different installers from the same script in Inno Setup?

The answer is simple: create two files for each release, but put the common stuff in a third file and #include it in the other two.

http://rickborup.blogspot.com/2006/09/inno-setup-include-directive.html

You can simply use

#ifdef DebugVersion
File: *.pdb ...
#endif

and then call the Inno compiler like this:

iscc.exe -DDebugVersion ...

I'd also add something like this so you get different output file names:

#ifdef DebugVersion
OutputBaseFileName=mysetup-dbg
#else
OutputBaseFileName=mysetup
#endif

Note that you'll probably need the InnoSetup precompiler for this, which, for some inexplicable reason, is not part of the default InnoSetup package. The easiest way to get it is to get the "Quick Start Pack" from the InnoSetup download page.