If you want to just do a build where the build artifacts don't pollute the source directory, the repository mechanism can help with that. Here's an example: checkout or unpack your project in the directory src, and then build it in build:

$ mkdir build
$ cd build
$ scons -Q -Y ../src
gcc -o foo.o -I. -I/path/to/src -c /path/to/src/foo.c
gcc -o foo foo.o
$ ls
foo  foo.o
    

It can become awkward to keep having to type -Y path-to-repo repeatedly. If so, the option can be placed in SCONSFLAGS.