Even when you give up on writing true "hybrid" code (i.e. "just write modules for the slow parts in C++", which is a gigantic pain), and instead try to write driver code that calls standalone compiled applications, you find yourself having to write a lot of duplicate code to parse/validate I/O on both sides of the language boundary. It sucks, and there's no way to make it not suck.
I'd go so far as to say that for problems where processing speed is a known requirement from the start, you should just give up on interpreted languages. Fast interpreted languages have been right around the corner for long as I've been writing code, but they sure seem to be taking their time.
Ruby provides some very useful features, but a lot of those come at rather high costs. Those costs are exacerbated if you do not understand how the internal components of the language are laid out, and the purpose behind this layout.
Ruby tries to be a lot of things to a lot of people, so then when people learn how to use it for one task they automatically assume that their skills will carry over. This sort of approach might work reasonably well with a straight-forward compiled language, but this it simply can't be that easy for an interpreted language like ruby, with it's reams of special context sensitive behaviour.
For example, consider the "pointers to pointers to pointers" complaint. Nothing is stopping you from having a low level C struct for all your performance sensitive data. Granted, you would have to write a ruby wrapper for this data for when you need to export it back out to ruby, but wrapper generation could be automated.
Sure, you could just say, "You know what. I'm just going to use C" but what if your project could really use some of those ruby features outside of the performance sensitive parts of the code? It's always a tradeoff.
There is SWIG support for Ruby, as well as the Ruby FFI implementation and RubyInline, offering various degrees of simplicity, but none of them are hard. The Ruby extension interface is more work, but even that is fairly simple to work with. I've taken C libraries and wrapped them in Ruby in minutes using SWIG for example.
Overall I often these days choose to write in Ruby first and replace even for applications that I intend to write the finished version of entirely in C. Prototyping in Ruby and rewriting in C once I have a working version is faster to me than iterating over a C version.
The fact that the speed-critical parts of your problem could be reduced to a "few, small bits" indicates that we're talking about entirely different things.
I was in a problem domain where writing the time-critical pieces in a different language meant ensuring that huge amounts of working-set data were available to that optimized code. Efficient access to that data meant storage in native format, which meant that supporting two languages would require a nasty I/O layer for the interpreted language. Not worth it.
And that's just for the problems where it was possible to consider using Perl/Python at all. For some problems, the memory overhead of Perl/Python data structures ruled out use on all but the smallest problems. Again, not worth it.
It's nice that the speed-critical parts of your problem were reducible to a few lines of code, but that's not often the case. For most real problems, I/O is a huge concern, and can't be dismissed just by pre-processing the input.
It's certainly doable, and definitely the right way to go if you want number crunching in a high-level language, but it's not a free lunch. It's certainly not a quick one-time conversion and then you can forget about it.
If more people thought of FFI/RPC/etc. as just another pipe-and-filter framework, they'd be less reluctant to write properly-defined, performance critical, pieces in a more performant environment.
Then again, your use of a profiler and FFI/pipe/whatever is a secret weapon that seems to be one of the things that separate 1x from 10x engineers. :-)
For many types of problems, putting the data into an efficient format before passing it to your C/C++ code is trivial in terms of both difficulty and time spent.
I prototyped everything in Ruby, profiled, and then rewrote a handful of the critical parts in C and C++.