I ended up solving my issue by using the GitSCM checkout with submodules disabled for the super project and then calling for a submodule update manually (required a credential helper on my build machine). Something like...
checkout([ $class: 'GitSCM', branches: [[name: "<Branch Name>"]], doGenerateSubmoduleConfigurations: false, extensions: [[$class: 'LocalBranch']] + [[$class: 'SubmoduleOption', disableSubmodules: true, parentCredentials: true, recursiveSubmodules: false, reference: '', trackingSubmodules: false]], submoduleCfg: [], userRemoteConfigs: [[credentialsId: '<ID>', url: '<url>']] ]) // Manual submodule update git submodule update --init --recursive

Just out of curiosity I've taken a look at what happens under the hood, and I've used [dtruss/strace][1] on each test.
C++
./a.out < in Saw 6512403 lines in 8 seconds. Crunch speed: 814050
syscalls `sudo dtruss -c ./a.out < in`
CALL COUNT __mac_syscall 1 <snip> open 6 pread 8 mprotect 17 mmap 22 stat64 30 read_nocancel 25958

Python
./a.py < in Read 6512402 lines in 1 seconds. LPS: 6512402
syscalls `sudo dtruss -c ./a.py < in`
CALL COUNT __mac_syscall 1 <snip> open 5 pread 8 mprotect 17 mmap 21 stat64 29
[1]: http://en.wikipedia.org/wiki/Strace